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1
treatment: siNT,cell line: OCI-LY1
413 E 69th Street, BB-1462
New York
USA
WCMC
Katerina,,Hatzi
ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mismatches were used for downstream analysis. Several reads mapping to the same exact location (clonal reads) were considered amplification artifact and were excluded from the analysis. Table S2 includes information of the total number of mapped reads that where used in our analysis. Read density tracks were visualized using the UCSC browser. ChIPseeqer peak detection algorithm (http://icb.med.cornell.edu/wiki/index.php/Elementolab/) was used for analyzing ChIP-seq data. Each read was in silico extended to 158bp based on the strand that it aligned to. Each ChIP-seq dataset was normalized to its corresponding input lane.,Genome_build: hg18,Supplementary_files_format_and_content: "Read_density-wig" files are wig tracks generated using ChIPseeqerMakeReadDensityTrack of the ChIPseqer package. (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerMakeReadDensityTrack).They represent the average ChIPseq read density, normalized to the total number of reads. Wgl tracks called "peaks" are the peak locations called for every experiment by our peakcaling algorithm and they were generated using ChIPseeqer (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_PeaksTrack)
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A’ bases were added to the 3’ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adapter ligation DNA was separated by electrophoresis and size selected by isolating a gel band of 250±25bp. This fragment range corresponds to a ChIP fragment range of about 158±25bp. Size selected fragments were PCR amplified for 15cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30s at 98oC, 15cycles of 10 at 98oC, 30s at 65oC,30s at 72oC and 5min extension at 75oC). Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment. RNAseq: Three ug of total RNA was isolated from OCI-Ly1 cells transfected using Nucleofector 96-well Shuttle system (Lonza) with siBCL6 (HSS100968) or siNT (46-2001) (Stealth RNAi, Invitrogen) at 24hrs and 48hrs after nucleofection. RNAeasy Plus Kit (Qiagen) that included a gDNA elimination step was used for RNA isolation. RNA concentration and purity were determined using Nanodrop (Thermo Scientific) and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries were generated using mRNA-seq sample prep kit by Illumina. Briefly, mRNA was selected by two rounds of purification using magnetic polydT beads and then fragmented. First strand synthesis was performed using random oligos and SupersciptIII (Invitrogen). After second strand synthesis a 200bp paired-end library was prepared following the Illumina paired-end library preparation protocol.
GSM1000981
Illumina HiSeq 1000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL15433
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX185895,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01163911,Named Annotation: NA000044218.1 (GSM1000981_OCI-LY1_48hrs_mRNAseq_3x_siNT_R1.bw)
GSM1000981
GSE29282
0
Human DLBCL cel line
Public on Aug 05 2013
Sep 10 2012
9606
OCI-LY1_48hrs_mRNAseq_3x_siNT_R1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX185895
https://www.ncbi.nlm.nih.gov/biosample/SAMN01163911
1
treatment: siNT,cell line: OCI-LY1
413 E 69th Street, BB-1462
New York
USA
WCMC
Katerina,,Hatzi
ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mismatches were used for downstream analysis. Several reads mapping to the same exact location (clonal reads) were considered amplification artifact and were excluded from the analysis. Table S2 includes information of the total number of mapped reads that where used in our analysis. Read density tracks were visualized using the UCSC browser. ChIPseeqer peak detection algorithm (http://icb.med.cornell.edu/wiki/index.php/Elementolab/) was used for analyzing ChIP-seq data. Each read was in silico extended to 158bp based on the strand that it aligned to. Each ChIP-seq dataset was normalized to its corresponding input lane.,Genome_build: hg18,Supplementary_files_format_and_content: "Read_density-wig" files are wig tracks generated using ChIPseeqerMakeReadDensityTrack of the ChIPseqer package. (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerMakeReadDensityTrack).They represent the average ChIPseq read density, normalized to the total number of reads. Wgl tracks called "peaks" are the peak locations called for every experiment by our peakcaling algorithm and they were generated using ChIPseeqer (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_PeaksTrack)
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A’ bases were added to the 3’ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adapter ligation DNA was separated by electrophoresis and size selected by isolating a gel band of 250±25bp. This fragment range corresponds to a ChIP fragment range of about 158±25bp. Size selected fragments were PCR amplified for 15cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30s at 98oC, 15cycles of 10 at 98oC, 30s at 65oC,30s at 72oC and 5min extension at 75oC). Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment. RNAseq: Three ug of total RNA was isolated from OCI-Ly1 cells transfected using Nucleofector 96-well Shuttle system (Lonza) with siBCL6 (HSS100968) or siNT (46-2001) (Stealth RNAi, Invitrogen) at 24hrs and 48hrs after nucleofection. RNAeasy Plus Kit (Qiagen) that included a gDNA elimination step was used for RNA isolation. RNA concentration and purity were determined using Nanodrop (Thermo Scientific) and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries were generated using mRNA-seq sample prep kit by Illumina. Briefly, mRNA was selected by two rounds of purification using magnetic polydT beads and then fragmented. First strand synthesis was performed using random oligos and SupersciptIII (Invitrogen). After second strand synthesis a 200bp paired-end library was prepared following the Illumina paired-end library preparation protocol.
GSM1000982
Illumina HiSeq 1000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL15433
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX185896,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01163912,Named Annotation: NA000044219.1 (GSM1000982_OCI-LY1_48hrs_mRNAseq_3x_siNT_R2.bw)
GSM1000982
GSE29282
0
Human DLBCL cel line
Public on Aug 05 2013
Sep 10 2012
9606
OCI-LY1_48hrs_mRNAseq_3x_siNT_R2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX185896
https://www.ncbi.nlm.nih.gov/biosample/SAMN01163912
1
treatment: siNT,cell line: OCI-LY1
413 E 69th Street, BB-1462
New York
USA
WCMC
Katerina,,Hatzi
ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mismatches were used for downstream analysis. Several reads mapping to the same exact location (clonal reads) were considered amplification artifact and were excluded from the analysis. Table S2 includes information of the total number of mapped reads that where used in our analysis. Read density tracks were visualized using the UCSC browser. ChIPseeqer peak detection algorithm (http://icb.med.cornell.edu/wiki/index.php/Elementolab/) was used for analyzing ChIP-seq data. Each read was in silico extended to 158bp based on the strand that it aligned to. Each ChIP-seq dataset was normalized to its corresponding input lane.,Genome_build: hg18,Supplementary_files_format_and_content: "Read_density-wig" files are wig tracks generated using ChIPseeqerMakeReadDensityTrack of the ChIPseqer package. (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerMakeReadDensityTrack).They represent the average ChIPseq read density, normalized to the total number of reads. Wgl tracks called "peaks" are the peak locations called for every experiment by our peakcaling algorithm and they were generated using ChIPseeqer (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_PeaksTrack)
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A’ bases were added to the 3’ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adapter ligation DNA was separated by electrophoresis and size selected by isolating a gel band of 250±25bp. This fragment range corresponds to a ChIP fragment range of about 158±25bp. Size selected fragments were PCR amplified for 15cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30s at 98oC, 15cycles of 10 at 98oC, 30s at 65oC,30s at 72oC and 5min extension at 75oC). Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment. RNAseq: Three ug of total RNA was isolated from OCI-Ly1 cells transfected using Nucleofector 96-well Shuttle system (Lonza) with siBCL6 (HSS100968) or siNT (46-2001) (Stealth RNAi, Invitrogen) at 24hrs and 48hrs after nucleofection. RNAeasy Plus Kit (Qiagen) that included a gDNA elimination step was used for RNA isolation. RNA concentration and purity were determined using Nanodrop (Thermo Scientific) and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries were generated using mRNA-seq sample prep kit by Illumina. Briefly, mRNA was selected by two rounds of purification using magnetic polydT beads and then fragmented. First strand synthesis was performed using random oligos and SupersciptIII (Invitrogen). After second strand synthesis a 200bp paired-end library was prepared following the Illumina paired-end library preparation protocol.
GSM1000983
Illumina HiSeq 1000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL15433
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX185897,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01163913,Named Annotation: NA000044220.1 (GSM1000983_OCI-LY1_48hrs_mRNAseq_3x_siNT_R3.bw)
GSM1000983
GSE29282
0
Human DLBCL cel line
Public on Aug 05 2013
Sep 10 2012
9606
OCI-LY1_48hrs_mRNAseq_3x_siNT_R3
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX185897
https://www.ncbi.nlm.nih.gov/biosample/SAMN01163913
1
treatment: siBCL6,cell line: OCI-LY1
413 E 69th Street, BB-1462
New York
USA
WCMC
Katerina,,Hatzi
ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mismatches were used for downstream analysis. Several reads mapping to the same exact location (clonal reads) were considered amplification artifact and were excluded from the analysis. Table S2 includes information of the total number of mapped reads that where used in our analysis. Read density tracks were visualized using the UCSC browser. ChIPseeqer peak detection algorithm (http://icb.med.cornell.edu/wiki/index.php/Elementolab/) was used for analyzing ChIP-seq data. Each read was in silico extended to 158bp based on the strand that it aligned to. Each ChIP-seq dataset was normalized to its corresponding input lane.,Genome_build: hg18,Supplementary_files_format_and_content: "Read_density-wig" files are wig tracks generated using ChIPseeqerMakeReadDensityTrack of the ChIPseqer package. (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerMakeReadDensityTrack).They represent the average ChIPseq read density, normalized to the total number of reads. Wgl tracks called "peaks" are the peak locations called for every experiment by our peakcaling algorithm and they were generated using ChIPseeqer (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_PeaksTrack)
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A’ bases were added to the 3’ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adapter ligation DNA was separated by electrophoresis and size selected by isolating a gel band of 250±25bp. This fragment range corresponds to a ChIP fragment range of about 158±25bp. Size selected fragments were PCR amplified for 15cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30s at 98oC, 15cycles of 10 at 98oC, 30s at 65oC,30s at 72oC and 5min extension at 75oC). Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment. RNAseq: Three ug of total RNA was isolated from OCI-Ly1 cells transfected using Nucleofector 96-well Shuttle system (Lonza) with siBCL6 (HSS100968) or siNT (46-2001) (Stealth RNAi, Invitrogen) at 24hrs and 48hrs after nucleofection. RNAeasy Plus Kit (Qiagen) that included a gDNA elimination step was used for RNA isolation. RNA concentration and purity were determined using Nanodrop (Thermo Scientific) and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries were generated using mRNA-seq sample prep kit by Illumina. Briefly, mRNA was selected by two rounds of purification using magnetic polydT beads and then fragmented. First strand synthesis was performed using random oligos and SupersciptIII (Invitrogen). After second strand synthesis a 200bp paired-end library was prepared following the Illumina paired-end library preparation protocol.
GSM1000984
Illumina HiSeq 1000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL15433
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX185898,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01163914,Named Annotation: NA000044221.1 (GSM1000984_OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R1.bw)
GSM1000984
GSE29282
0.004366
Human DLBCL cel line
Public on Aug 05 2013
Sep 10 2012
9606
OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX185898
https://www.ncbi.nlm.nih.gov/biosample/SAMN01163914
1
treatment: siBCL6,cell line: OCI-LY1
413 E 69th Street, BB-1462
New York
USA
WCMC
Katerina,,Hatzi
ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mismatches were used for downstream analysis. Several reads mapping to the same exact location (clonal reads) were considered amplification artifact and were excluded from the analysis. Table S2 includes information of the total number of mapped reads that where used in our analysis. Read density tracks were visualized using the UCSC browser. ChIPseeqer peak detection algorithm (http://icb.med.cornell.edu/wiki/index.php/Elementolab/) was used for analyzing ChIP-seq data. Each read was in silico extended to 158bp based on the strand that it aligned to. Each ChIP-seq dataset was normalized to its corresponding input lane.,Genome_build: hg18,Supplementary_files_format_and_content: "Read_density-wig" files are wig tracks generated using ChIPseeqerMakeReadDensityTrack of the ChIPseqer package. (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerMakeReadDensityTrack).They represent the average ChIPseq read density, normalized to the total number of reads. Wgl tracks called "peaks" are the peak locations called for every experiment by our peakcaling algorithm and they were generated using ChIPseeqer (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_PeaksTrack)
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A’ bases were added to the 3’ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adapter ligation DNA was separated by electrophoresis and size selected by isolating a gel band of 250±25bp. This fragment range corresponds to a ChIP fragment range of about 158±25bp. Size selected fragments were PCR amplified for 15cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30s at 98oC, 15cycles of 10 at 98oC, 30s at 65oC,30s at 72oC and 5min extension at 75oC). Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment. RNAseq: Three ug of total RNA was isolated from OCI-Ly1 cells transfected using Nucleofector 96-well Shuttle system (Lonza) with siBCL6 (HSS100968) or siNT (46-2001) (Stealth RNAi, Invitrogen) at 24hrs and 48hrs after nucleofection. RNAeasy Plus Kit (Qiagen) that included a gDNA elimination step was used for RNA isolation. RNA concentration and purity were determined using Nanodrop (Thermo Scientific) and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries were generated using mRNA-seq sample prep kit by Illumina. Briefly, mRNA was selected by two rounds of purification using magnetic polydT beads and then fragmented. First strand synthesis was performed using random oligos and SupersciptIII (Invitrogen). After second strand synthesis a 200bp paired-end library was prepared following the Illumina paired-end library preparation protocol.
GSM1000985
Illumina HiSeq 1000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL15433
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX185899,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01163915,Named Annotation: NA000044222.1 (GSM1000985_OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R2.bw)
GSM1000985
GSE29282
0
Human DLBCL cel line
Public on Aug 05 2013
Sep 10 2012
9606
OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX185899
https://www.ncbi.nlm.nih.gov/biosample/SAMN01163915
1
treatment: siBCL6,cell line: OCI-LY1
413 E 69th Street, BB-1462
New York
USA
WCMC
Katerina,,Hatzi
ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mismatches were used for downstream analysis. Several reads mapping to the same exact location (clonal reads) were considered amplification artifact and were excluded from the analysis. Table S2 includes information of the total number of mapped reads that where used in our analysis. Read density tracks were visualized using the UCSC browser. ChIPseeqer peak detection algorithm (http://icb.med.cornell.edu/wiki/index.php/Elementolab/) was used for analyzing ChIP-seq data. Each read was in silico extended to 158bp based on the strand that it aligned to. Each ChIP-seq dataset was normalized to its corresponding input lane.,Genome_build: hg18,Supplementary_files_format_and_content: "Read_density-wig" files are wig tracks generated using ChIPseeqerMakeReadDensityTrack of the ChIPseqer package. (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerMakeReadDensityTrack).They represent the average ChIPseq read density, normalized to the total number of reads. Wgl tracks called "peaks" are the peak locations called for every experiment by our peakcaling algorithm and they were generated using ChIPseeqer (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_PeaksTrack)
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A’ bases were added to the 3’ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adapter ligation DNA was separated by electrophoresis and size selected by isolating a gel band of 250±25bp. This fragment range corresponds to a ChIP fragment range of about 158±25bp. Size selected fragments were PCR amplified for 15cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30s at 98oC, 15cycles of 10 at 98oC, 30s at 65oC,30s at 72oC and 5min extension at 75oC). Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment. RNAseq: Three ug of total RNA was isolated from OCI-Ly1 cells transfected using Nucleofector 96-well Shuttle system (Lonza) with siBCL6 (HSS100968) or siNT (46-2001) (Stealth RNAi, Invitrogen) at 24hrs and 48hrs after nucleofection. RNAeasy Plus Kit (Qiagen) that included a gDNA elimination step was used for RNA isolation. RNA concentration and purity were determined using Nanodrop (Thermo Scientific) and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries were generated using mRNA-seq sample prep kit by Illumina. Briefly, mRNA was selected by two rounds of purification using magnetic polydT beads and then fragmented. First strand synthesis was performed using random oligos and SupersciptIII (Invitrogen). After second strand synthesis a 200bp paired-end library was prepared following the Illumina paired-end library preparation protocol.
GSM1000986
Illumina HiSeq 1000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL15433
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX185900,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01163916,Named Annotation: NA000044223.1 (GSM1000986_OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R3.bw)
GSM1000986
GSE29282
0
Human DLBCL cel line
Public on Aug 05 2013
Sep 10 2012
9606
OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R3
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX185900
https://www.ncbi.nlm.nih.gov/biosample/SAMN01163916
1
spike-in hsa-mir-147: 0.1,spike-in hsa-mir-211: 1,spike-in hsa-mir-219-5p: 10,spike-in hsa-mir-338-3p: 0.1,spike-in hsa-mir-383: 1,spike-in hsa-mir-429: 10,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-mir-383: 0,o-methyl spike-in hsa-mir-429: 0
P.O.B. 26
Rehovot
Israel
Weizmann Institute of Science
Dena,,Leshkowitz
Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).,The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA,Genome_build: mirbase release 18,Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
GSM1002540
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186158,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166092
GSM1002540
GSE40819,GSE40820
0.00513
placenta
Public on Mar 01 2013
Sep 12 2012
9606
mix1-rep1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186158
https://www.ncbi.nlm.nih.gov/biosample/SAMN01166092
1
spike-in hsa-mir-147: 1,spike-in hsa-mir-211: 10,spike-in hsa-mir-219-5p: 0.1,spike-in hsa-mir-338-3p: 1,spike-in hsa-mir-383: 10,spike-in hsa-mir-429: 0.1,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-mir-383: 0,o-methyl spike-in hsa-mir-429: 0
P.O.B. 26
Rehovot
Israel
Weizmann Institute of Science
Dena,,Leshkowitz
Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).,The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA,Genome_build: mirbase release 18,Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
GSM1002541
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186159,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166093
GSM1002541
GSE40819,GSE40820
0
placenta
Public on Mar 01 2013
Sep 12 2012
9606
mix2-rep1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186159
https://www.ncbi.nlm.nih.gov/biosample/SAMN01166093
1
spike-in hsa-mir-147: 10,spike-in hsa-mir-211: 0.1,spike-in hsa-mir-219-5p: 1,spike-in hsa-mir-338-3p: 10,spike-in hsa-mir-383: 0.1,spike-in hsa-mir-429: 1,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-mir-383: 0,o-methyl spike-in hsa-mir-429: 0
P.O.B. 26
Rehovot
Israel
Weizmann Institute of Science
Dena,,Leshkowitz
Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).,The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA,Genome_build: mirbase release 18,Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
GSM1002542
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186160,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166094
GSM1002542
GSE40819,GSE40820
0.130026
placenta
Public on Mar 01 2013
Sep 12 2012
9606
mix3-rep1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186160
https://www.ncbi.nlm.nih.gov/biosample/SAMN01166094
1
spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 0.1,o-methyl spike-in hsa-mir-211: 1,o-methyl spike-in hsa-mir-219-5p: 10,precursor spike-in hsa-mir-338-3p: 0.1,precursor spike-in hsa-mir-383: 1,o-methyl spike-in hsa-mir-429: 10
P.O.B. 26
Rehovot
Israel
Weizmann Institute of Science
Dena,,Leshkowitz
Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).,The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA,Genome_build: mirbase release 18,Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
GSM1002543
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186161,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166095
GSM1002543
GSE40819,GSE40820
0.143913
placenta
Public on Mar 01 2013
Sep 12 2012
9606
mix4-rep1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186161
https://www.ncbi.nlm.nih.gov/biosample/SAMN01166095
1
spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 1,o-methyl spike-in hsa-mir-211: 10,o-methyl spike-in hsa-mir-219-5p: 0.1,precursor spike-in hsa-mir-338-3p: 1,precursor spike-in hsa-mir-383: 10,o-methyl spike-in hsa-mir-429: 0.1
P.O.B. 26
Rehovot
Israel
Weizmann Institute of Science
Dena,,Leshkowitz
Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).,The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA,Genome_build: mirbase release 18,Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
GSM1002544
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186162,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166096
GSM1002544
GSE40819,GSE40820
0.095942
placenta
Public on Mar 01 2013
Sep 12 2012
9606
mix5-rep1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186162
https://www.ncbi.nlm.nih.gov/biosample/SAMN01166096
1
spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 10,o-methyl spike-in hsa-mir-211: 0.1,o-methyl spike-in hsa-mir-219-5p: 1,precursor spike-in hsa-mir-338-3p: 10,precursor spike-in hsa-mir-383: 0.1,o-methyl spike-in hsa-mir-429: 1
P.O.B. 26
Rehovot
Israel
Weizmann Institute of Science
Dena,,Leshkowitz
Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).,The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA,Genome_build: mirbase release 18,Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
GSM1002545
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186163,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166097
GSM1002545
GSE40819,GSE40820
0.161421
placenta
Public on Mar 01 2013
Sep 12 2012
9606
mix6-rep1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186163
https://www.ncbi.nlm.nih.gov/biosample/SAMN01166097
1
spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-mir-383: 0,o-methyl spike-in hsa-mir-429: 0
P.O.B. 26
Rehovot
Israel
Weizmann Institute of Science
Dena,,Leshkowitz
Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).,The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA,Genome_build: mirbase release 18,Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
GSM1002546
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186164,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166098
GSM1002546
GSE40819,GSE40820
0.092059
placenta
Public on Mar 01 2013
Sep 12 2012
9606
mix7-rep1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186164
https://www.ncbi.nlm.nih.gov/biosample/SAMN01166098
1
spike-in hsa-mir-147: 0.1,spike-in hsa-mir-211: 1,spike-in hsa-mir-219-5p: 10,spike-in hsa-mir-338-3p: 0.1,spike-in hsa-mir-383: 1,spike-in hsa-mir-429: 10,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-mir-383: 0,o-methyl spike-in hsa-mir-429: 0
P.O.B. 26
Rehovot
Israel
Weizmann Institute of Science
Dena,,Leshkowitz
Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).,The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA,Genome_build: mirbase release 18,Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
GSM1002547
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186165,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166099
GSM1002547
GSE40819,GSE40820
0
placenta
Public on Mar 01 2013
Sep 12 2012
9606
mix1-rep2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186165
https://www.ncbi.nlm.nih.gov/biosample/SAMN01166099
1
spike-in hsa-mir-147: 1,spike-in hsa-mir-211: 10,spike-in hsa-mir-219-5p: 0.1,spike-in hsa-mir-338-3p: 1,spike-in hsa-mir-383: 10,spike-in hsa-mir-429: 0.1,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-mir-383: 0,o-methyl spike-in hsa-mir-429: 0
P.O.B. 26
Rehovot
Israel
Weizmann Institute of Science
Dena,,Leshkowitz
Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).,The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA,Genome_build: mirbase release 18,Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
GSM1002548
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186166,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166100
GSM1002548
GSE40819,GSE40820
0.049992
placenta
Public on Mar 01 2013
Sep 12 2012
9606
mix2-rep2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186166
https://www.ncbi.nlm.nih.gov/biosample/SAMN01166100
1
spike-in hsa-mir-147: 10,spike-in hsa-mir-211: 0.1,spike-in hsa-mir-219-5p: 1,spike-in hsa-mir-338-3p: 10,spike-in hsa-mir-383: 0.1,spike-in hsa-mir-429: 1,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-mir-383: 0,o-methyl spike-in hsa-mir-429: 0
P.O.B. 26
Rehovot
Israel
Weizmann Institute of Science
Dena,,Leshkowitz
Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).,The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA,Genome_build: mirbase release 18,Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
GSM1002549
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186167,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166101
GSM1002549
GSE40819,GSE40820
0.107731
placenta
Public on Mar 01 2013
Sep 12 2012
9606
mix3-rep2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186167
https://www.ncbi.nlm.nih.gov/biosample/SAMN01166101
1
spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 0.1,o-methyl spike-in hsa-mir-211: 1,o-methyl spike-in hsa-mir-219-5p: 10,precursor spike-in hsa-mir-338-3p: 0.1,precursor spike-in hsa-mir-383: 1,o-methyl spike-in hsa-mir-429: 10
P.O.B. 26
Rehovot
Israel
Weizmann Institute of Science
Dena,,Leshkowitz
Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).,The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA,Genome_build: mirbase release 18,Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
GSM1002550
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186168,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166102
GSM1002550
GSE40819,GSE40820
0
placenta
Public on Mar 01 2013
Sep 12 2012
9606
mix4-rep2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186168
https://www.ncbi.nlm.nih.gov/biosample/SAMN01166102
1
spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 1,o-methyl spike-in hsa-mir-211: 10,o-methyl spike-in hsa-mir-219-5p: 0.1,precursor spike-in hsa-mir-338-3p: 1,precursor spike-in hsa-mir-383: 10,o-methyl spike-in hsa-mir-429: 0.1
P.O.B. 26
Rehovot
Israel
Weizmann Institute of Science
Dena,,Leshkowitz
Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).,The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA,Genome_build: mirbase release 18,Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
GSM1002551
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186169,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166103
GSM1002551
GSE40819,GSE40820
0.02033
placenta
Public on Mar 01 2013
Sep 12 2012
9606
mix5-rep2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186169
https://www.ncbi.nlm.nih.gov/biosample/SAMN01166103
1
spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 10,o-methyl spike-in hsa-mir-211: 0.1,o-methyl spike-in hsa-mir-219-5p: 1,precursor spike-in hsa-mir-338-3p: 10,precursor spike-in hsa-mir-383: 0.1,o-methyl spike-in hsa-mir-429: 1
P.O.B. 26
Rehovot
Israel
Weizmann Institute of Science
Dena,,Leshkowitz
Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).,The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA,Genome_build: mirbase release 18,Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
GSM1002552
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186170,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166104
GSM1002552
GSE40819,GSE40820
0.143934
placenta
Public on Mar 01 2013
Sep 12 2012
9606
mix6-rep2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186170
https://www.ncbi.nlm.nih.gov/biosample/SAMN01166104
1
spike-in hsa-mir-147: 0,spike-in hsa-mir-211: 0,spike-in hsa-mir-219-5p: 0,spike-in hsa-mir-338-3p: 0,spike-in hsa-mir-383: 0,spike-in hsa-mir-429: 0,precursor spike-in hsa-mir-147: 0,o-methyl spike-in hsa-mir-211: 0,o-methyl spike-in hsa-mir-219-5p: 0,precursor spike-in hsa-mir-338-3p: 0,precursor spike-in hsa-mir-383: 0,o-methyl spike-in hsa-mir-429: 0
P.O.B. 26
Rehovot
Israel
Weizmann Institute of Science
Dena,,Leshkowitz
Basecalls performed using CASAVA version 1.8.1,Adaptors were removed and then collapsed into tags and quantified.,Tags that appeared at a frequency of 5 or more reads per library were normalized to reads per million (rpm).,The tags were annotated using the best hit of BLAST 2.2.23 (-S -e 0.01 options) and run against human mature miRNA databases (downloaded from mirbase.org, release 18).,The frequency of reads matching each miRNAs was calculated by summing the frequency of all the isoforms matching the miRNA,Genome_build: mirbase release 18,Supplementary_files_format_and_content: .txt file with rpm values for each miRNA
Commercial human placenta RNA was purchased from Ambion (AM7950) in two lots: 03070032 and 1004005. Small RNA library construction from 5 ug total RNA of each of the 14 samples was carried out using illumina TruSeq smRNA Sample Prep Kit (San-Diego, CA, USA), according to the manufacturer’s instructions. Briefly, 3` adapter was ligated to total RNA using RNL2, followed by 5’ adapter ligation, using T4 ligase. Reverse transcription with SuperScript II generated cDNA which was then PCR-amplified and size-selected on a gel and then purified. Sequencing was performed on two lanes of HiSeq 2000 using v2 clustering and sequencing reagents; seven libraries were multiplexed on each lane.
GSM1002553
Illumina HiSeq 2000
May 15 2019
size fractionation
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186171,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01166105
GSM1002553
GSE40819,GSE40820
0.03988
placenta
Public on Mar 01 2013
Sep 12 2012
9606
mix7-rep2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186171
https://www.ncbi.nlm.nih.gov/biosample/SAMN01166105
1
strategy: iCLIP-Seq,cell line: HeLa,clip antibody: CstF64
B228 Med Sci I
Irvine
USA
University of California, Irvine
Yongsheng,,Shi
iCLIP-seq: 1. Raw reads were demultiplexed using the sequencing barcode unique to each replicate and an additional random trinucleotide identifying individual DNA molecules was clipped but kept as metadata; 2. Reads with quality less than 20 for 10% or more of the bases were removed.3. We mapped the remaining reads to build hg19 of the human genome using bowtie,iCLIP-seq reads were mapped to hg19 using Bowtie,Direct RNA sequencing: Reads were filtered and mapped to hg19 using indexDPgenomic tool in Helisphere (www.Helicosbio.com),Genome_build: hg19,Supplementary_files_format_and_content: bed format
iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes; for direct RNA sequencing, RNAs were extracted from cells using Trizol reagent (Invitrogen),iCLIP-seq libraries were prepared as described by Konig et al, NSMB (2010) 17: 909; the antibody used was purchased from Bethyl Laboratories (Cat#: A301-092A; lot #: A301-092A-1),iCLIP-seq library strategy was the same as by Konig et al, NSMB (2010) 17: 909.
GSM1003587
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186536,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01173953
GSM1003587
GSE40859
0.064095
HeLa
Public on Oct 01 2012
Sep 13 2012
9606
CstF64-iCLIP rep1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186536
https://www.ncbi.nlm.nih.gov/biosample/SAMN01173953
1
strategy: iCLIP-Seq,cell line: HeLa,clip antibody: CstF64
B228 Med Sci I
Irvine
USA
University of California, Irvine
Yongsheng,,Shi
iCLIP-seq: 1. Raw reads were demultiplexed using the sequencing barcode unique to each replicate and an additional random trinucleotide identifying individual DNA molecules was clipped but kept as metadata; 2. Reads with quality less than 20 for 10% or more of the bases were removed.3. We mapped the remaining reads to build hg19 of the human genome using bowtie,iCLIP-seq reads were mapped to hg19 using Bowtie,Direct RNA sequencing: Reads were filtered and mapped to hg19 using indexDPgenomic tool in Helisphere (www.Helicosbio.com),Genome_build: hg19,Supplementary_files_format_and_content: bed format
iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes; for direct RNA sequencing, RNAs were extracted from cells using Trizol reagent (Invitrogen),iCLIP-seq libraries were prepared as described by Konig et al, NSMB (2010) 17: 909; the antibody used was purchased from Bethyl Laboratories (Cat#: A301-092A; lot #: A301-092A-1),iCLIP-seq library strategy was the same as by Konig et al, NSMB (2010) 17: 909.
GSM1003588
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186537,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01173954
GSM1003588
GSE40859
0.089459
HeLa
Public on Oct 01 2012
Sep 13 2012
9606
CstF64-iCLIP rep2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186537
https://www.ncbi.nlm.nih.gov/biosample/SAMN01173954
1
strategy: iCLIP-Seq,cell line: HeLa,clip antibody: CstF64
B228 Med Sci I
Irvine
USA
University of California, Irvine
Yongsheng,,Shi
iCLIP-seq: 1. Raw reads were demultiplexed using the sequencing barcode unique to each replicate and an additional random trinucleotide identifying individual DNA molecules was clipped but kept as metadata; 2. Reads with quality less than 20 for 10% or more of the bases were removed.3. We mapped the remaining reads to build hg19 of the human genome using bowtie,iCLIP-seq reads were mapped to hg19 using Bowtie,Direct RNA sequencing: Reads were filtered and mapped to hg19 using indexDPgenomic tool in Helisphere (www.Helicosbio.com),Genome_build: hg19,Supplementary_files_format_and_content: bed format
iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes; for direct RNA sequencing, RNAs were extracted from cells using Trizol reagent (Invitrogen),iCLIP-seq libraries were prepared as described by Konig et al, NSMB (2010) 17: 909; the antibody used was purchased from Bethyl Laboratories (Cat#: A301-092A; lot #: A301-092A-1),iCLIP-seq library strategy was the same as by Konig et al, NSMB (2010) 17: 909.
GSM1003589
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX186538,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01173955
GSM1003589
GSE40859
0.073131
HeLa
Public on Oct 01 2012
Sep 13 2012
9606
CstF64-iCLIP rep3
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX186538
https://www.ncbi.nlm.nih.gov/biosample/SAMN01173955
1
cell type: H1 embryonic stem cells
9 Cambridge Center
Cambridge
USA
Whitehead Institute for Biomedical Research
Richard,A,Young
For RNA-Seq samples. all sequenced reads were aligned to the human genome (Hg18) using the spliced read aligner TopHat version V1.4.0 (Trapnell et al. 2009). The paired end reads were aligned using "Bowtie -v" option for initial read mapping along with --microexon-search and --coverage-search options for identifying splicing.,supplementary_files_format_and_content: RPKM: The average (combining hESC or 48hr replicates) reads per kilobase of exonic length per million (RPKM) for each gene or lncRNA (see manuscript for details) was calculated and reported.,Images analysis and base calling was done using the solexa pipeline.,Genome_build: hg18
Total RNA was purified using mirVana miRNA isolation kit (Life Technologies) following the manufacturer instructions and treated with DNA-free™ DNase I (Ambion). Polyadenylated RNA was purified from the total RNA by two rounds of selection using Dynabeads® mRNA Purification Kit for mRNA Purification from Total RNA (Life Technologies) following the manufacturer instructions and sequenced using a modified Illumina mRNA-Seq protocol. Polyadenylated RNA was fragmented and sequenced according to modified version of standard Illumina RNA-seq protocol. First strand cDNA synthesis was performed with random hexamers and Superscript III reverse transcriptase. Second strand cDNA synthesis was performed using RNAse H and DNA Polymerase I. In the second-strand synthesis reaction, dTTP was replaced with dUTP. Following cDNA synthesis, the double stranded products were end repaired, a single “A” base was added, and Illumina PE adaptors were ligated onto the cDNA products. The ligation products with an average size of 300 bp were purified using agarose gel electrophoresis. Following gel purification, the strand of cDNA containing dUTP was selectively destroyed during incubation of purified double-stranded DNA with HK-UNG (Epicentre). The adapter ligated single-stranded cDNA was then amplified with 15 cycles of PCR and PCR products were purified using gel electrophoresis. RNA-seq libraries were sequenced on Illumina HiSeq 2000.
GSM1006725
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
Reanalyzed by: GSE76586,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX188846,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01179603
GSM1006725
GSE41009
0.070537
RNA-seq H1-hESC
Public on Jan 02 2013
Sep 19 2012
9606
RNA_Seq_hESC_2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX188846
https://www.ncbi.nlm.nih.gov/biosample/SAMN01179603
1
cell type: H1 embryonic stem cells,drug treatment: Activin,drug concentration: 50ng/ml,duration of treatment: 48hr
9 Cambridge Center
Cambridge
USA
Whitehead Institute for Biomedical Research
Richard,A,Young
For RNA-Seq samples. all sequenced reads were aligned to the human genome (Hg18) using the spliced read aligner TopHat version V1.4.0 (Trapnell et al. 2009). The paired end reads were aligned using "Bowtie -v" option for initial read mapping along with --microexon-search and --coverage-search options for identifying splicing.,supplementary_files_format_and_content: RPKM: The average (combining hESC or 48hr replicates) reads per kilobase of exonic length per million (RPKM) for each gene or lncRNA (see manuscript for details) was calculated and reported.,Images analysis and base calling was done using the solexa pipeline.,Genome_build: hg18
Total RNA was purified using mirVana miRNA isolation kit (Life Technologies) following the manufacturer instructions and treated with DNA-free™ DNase I (Ambion). Polyadenylated RNA was purified from the total RNA by two rounds of selection using Dynabeads® mRNA Purification Kit for mRNA Purification from Total RNA (Life Technologies) following the manufacturer instructions and sequenced using a modified Illumina mRNA-Seq protocol. Polyadenylated RNA was fragmented and sequenced according to modified version of standard Illumina RNA-seq protocol. First strand cDNA synthesis was performed with random hexamers and Superscript III reverse transcriptase. Second strand cDNA synthesis was performed using RNAse H and DNA Polymerase I. In the second-strand synthesis reaction, dTTP was replaced with dUTP. Following cDNA synthesis, the double stranded products were end repaired, a single “A” base was added, and Illumina PE adaptors were ligated onto the cDNA products. The ligation products with an average size of 300 bp were purified using agarose gel electrophoresis. Following gel purification, the strand of cDNA containing dUTP was selectively destroyed during incubation of purified double-stranded DNA with HK-UNG (Epicentre). The adapter ligated single-stranded cDNA was then amplified with 15 cycles of PCR and PCR products were purified using gel electrophoresis. RNA-seq libraries were sequenced on Illumina HiSeq 2000.
GSM1006726
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
Reanalyzed by: GSE76586,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX188847,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01179604
GSM1006726
GSE41009
0.136725
RNA-seq H1-hESC-48hr-Activin
Public on Jan 02 2013
Sep 19 2012
9606
RNA_Seq_48hr_1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX188847
https://www.ncbi.nlm.nih.gov/biosample/SAMN01179604
1
cell type: H1 embryonic stem cells,drug treatment: Activin,drug concentration: 50ng/ml,duration of treatment: 48hr
9 Cambridge Center
Cambridge
USA
Whitehead Institute for Biomedical Research
Richard,A,Young
For RNA-Seq samples. all sequenced reads were aligned to the human genome (Hg18) using the spliced read aligner TopHat version V1.4.0 (Trapnell et al. 2009). The paired end reads were aligned using "Bowtie -v" option for initial read mapping along with --microexon-search and --coverage-search options for identifying splicing.,supplementary_files_format_and_content: RPKM: The average (combining hESC or 48hr replicates) reads per kilobase of exonic length per million (RPKM) for each gene or lncRNA (see manuscript for details) was calculated and reported.,Images analysis and base calling was done using the solexa pipeline.,Genome_build: hg18
Total RNA was purified using mirVana miRNA isolation kit (Life Technologies) following the manufacturer instructions and treated with DNA-free™ DNase I (Ambion). Polyadenylated RNA was purified from the total RNA by two rounds of selection using Dynabeads® mRNA Purification Kit for mRNA Purification from Total RNA (Life Technologies) following the manufacturer instructions and sequenced using a modified Illumina mRNA-Seq protocol. Polyadenylated RNA was fragmented and sequenced according to modified version of standard Illumina RNA-seq protocol. First strand cDNA synthesis was performed with random hexamers and Superscript III reverse transcriptase. Second strand cDNA synthesis was performed using RNAse H and DNA Polymerase I. In the second-strand synthesis reaction, dTTP was replaced with dUTP. Following cDNA synthesis, the double stranded products were end repaired, a single “A” base was added, and Illumina PE adaptors were ligated onto the cDNA products. The ligation products with an average size of 300 bp were purified using agarose gel electrophoresis. Following gel purification, the strand of cDNA containing dUTP was selectively destroyed during incubation of purified double-stranded DNA with HK-UNG (Epicentre). The adapter ligated single-stranded cDNA was then amplified with 15 cycles of PCR and PCR products were purified using gel electrophoresis. RNA-seq libraries were sequenced on Illumina HiSeq 2000.
GSM1006727
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
Reanalyzed by: GSE76586,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX188848,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01179605
GSM1006727
GSE41009
0.199196
RNA-seq H1-hESC-48hr-Activin
Public on Jan 02 2013
Sep 19 2012
9606
RNA_Seq_48hr_2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX188848
https://www.ncbi.nlm.nih.gov/biosample/SAMN01179605
1
cell type: Primary Human Umbilical Vein Endothelial Cells,passages: P3-6,treatment: VEGF,time: 0h
10 Shattuck St
Boston
USA
Harvard Medical School
Peter,J,Park
All ChIP-seq and Dnase-seqexperiments were aligned against hg19 using bowtie with the -m 1 option,All RNA-seq experiments were aligned against hg19 using tophat with the standard parameters and using Ensembl GRCH37 version 65 as a reference transcript database,FPKM for all RNA-seq experiments were performed using cufflinks and cuffdiff using the -T option (for time series) and using Ensembl GRCh37 version 65 as a reference transcript annotation (no novel assembly),Genome_build: hg19,Supplementary_files_format_and_content: The processed FPKM file is CSV file with each row a different Ensembl gene that has the FPKM at each of the 4 time points,Supplementary_files_format_and_content: The BED files for the ChIP-seq and Dnase I samples are all the aligned, non-filtered reads
Illumina multiplex library protocol modified to use 2 rather than 3 primers; DHS-seq protocol using modified, indexed primers.
GSM1009635
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX189728,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01731041
GSM1009635
GSE41166
0.002183
Primary Human Umbilical Vein Endothelial Cells
Public on Mar 31 2013
Sep 26 2012
9606
RNA-seq Hour 0
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX189728
https://www.ncbi.nlm.nih.gov/biosample/SAMN01731041
1
cell type: Primary Human Umbilical Vein Endothelial Cells,passages: P3-6,treatment: VEGF,time: 1h
10 Shattuck St
Boston
USA
Harvard Medical School
Peter,J,Park
All ChIP-seq and Dnase-seqexperiments were aligned against hg19 using bowtie with the -m 1 option,All RNA-seq experiments were aligned against hg19 using tophat with the standard parameters and using Ensembl GRCH37 version 65 as a reference transcript database,FPKM for all RNA-seq experiments were performed using cufflinks and cuffdiff using the -T option (for time series) and using Ensembl GRCh37 version 65 as a reference transcript annotation (no novel assembly),Genome_build: hg19,Supplementary_files_format_and_content: The processed FPKM file is CSV file with each row a different Ensembl gene that has the FPKM at each of the 4 time points,Supplementary_files_format_and_content: The BED files for the ChIP-seq and Dnase I samples are all the aligned, non-filtered reads
Illumina multiplex library protocol modified to use 2 rather than 3 primers; DHS-seq protocol using modified, indexed primers.
GSM1009636
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX189729,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01731042
GSM1009636
GSE41166
0.012346
Primary Human Umbilical Vein Endothelial Cells
Public on Mar 31 2013
Sep 26 2012
9606
RNA-seq Hour 1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX189729
https://www.ncbi.nlm.nih.gov/biosample/SAMN01731042
1
cell type: Primary Human Umbilical Vein Endothelial Cells,passages: P3-6,treatment: VEGF,time: 4h
10 Shattuck St
Boston
USA
Harvard Medical School
Peter,J,Park
All ChIP-seq and Dnase-seqexperiments were aligned against hg19 using bowtie with the -m 1 option,All RNA-seq experiments were aligned against hg19 using tophat with the standard parameters and using Ensembl GRCH37 version 65 as a reference transcript database,FPKM for all RNA-seq experiments were performed using cufflinks and cuffdiff using the -T option (for time series) and using Ensembl GRCh37 version 65 as a reference transcript annotation (no novel assembly),Genome_build: hg19,Supplementary_files_format_and_content: The processed FPKM file is CSV file with each row a different Ensembl gene that has the FPKM at each of the 4 time points,Supplementary_files_format_and_content: The BED files for the ChIP-seq and Dnase I samples are all the aligned, non-filtered reads
Illumina multiplex library protocol modified to use 2 rather than 3 primers; DHS-seq protocol using modified, indexed primers.
GSM1009637
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX189730,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01731043
GSM1009637
GSE41166
0.008229
Primary Human Umbilical Vein Endothelial Cells
Public on Mar 31 2013
Sep 26 2012
9606
RNA-seq Hour 4
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX189730
https://www.ncbi.nlm.nih.gov/biosample/SAMN01731043
1
cell type: Primary Human Umbilical Vein Endothelial Cells,passages: P3-6,treatment: VEGF,time: 12h
10 Shattuck St
Boston
USA
Harvard Medical School
Peter,J,Park
All ChIP-seq and Dnase-seqexperiments were aligned against hg19 using bowtie with the -m 1 option,All RNA-seq experiments were aligned against hg19 using tophat with the standard parameters and using Ensembl GRCH37 version 65 as a reference transcript database,FPKM for all RNA-seq experiments were performed using cufflinks and cuffdiff using the -T option (for time series) and using Ensembl GRCh37 version 65 as a reference transcript annotation (no novel assembly),Genome_build: hg19,Supplementary_files_format_and_content: The processed FPKM file is CSV file with each row a different Ensembl gene that has the FPKM at each of the 4 time points,Supplementary_files_format_and_content: The BED files for the ChIP-seq and Dnase I samples are all the aligned, non-filtered reads
Illumina multiplex library protocol modified to use 2 rather than 3 primers; DHS-seq protocol using modified, indexed primers.
GSM1009638
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX189731,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01731044
GSM1009638
GSE41166
0.011829
Primary Human Umbilical Vein Endothelial Cells
Public on Mar 31 2013
Sep 26 2012
9606
RNA-seq Hour 12
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX189731
https://www.ncbi.nlm.nih.gov/biosample/SAMN01731044
1
cell line: HL60,rna fraction: Total RNA
Craig L. Dobbin Genetics Research Centre,
St. John's
Canada
Memorial University of Newfoundland
Touati,,Benoukraf
Bases were called using Casava 1.8.4 with default settings.,76-bp paired-end reads were aligned to human genome (hg19) using tophat 2.0.2 with default settings and without a reference assembly.,Assemblies were generated using Cufflinks 2.0.2 again, without reference assembly,Overlap with DNMT1-RIP-Seq was calculated using Bedtools.,Genome_build: hg19,Supplementary_files_format_and_content: Whole-transcriptome .gtf assemblies of Total and polyA(-) RNA samples, including FPKM values.
Total RNA was extracted with TRI REAGENT® (MRC). Total RNA was extracted with TRI Reagent® (MRC). RNA samples were treated with DNase I (10 U of DNase I (Roche) per 3 ug of total RNA; 37ºC for one hour; in the presence of RNase inhibitor). Non-polyadenylated RNA fractions were selected with the MicroPoly (A) PuristTM purification kit (Ambion). Total and not-polyadenylated RNA were depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit (cat. # MRZG126 Epicentre).,Double stranded cDNA libraries were constructed using ScriptSeq™ v2 RNA-Seq Library Preparation Kit (cat. # SSV21106 Epicentre) followed by Duplex Specific Nuclease (DSN) normalization (Evrogen, EA001). DSN treated libraries were subjected to final size-selection in 3% agarose gel. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). Libraries were sequenced (1/lane) on a HiSeq 2000 Illumina instrument.
GSM1013480
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX190848,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01737708
GSM1013480
GSE32260,GSE41279
0.065361
Myeloid Leukemia
Public on Dec 01 2012
Oct 02 2012
9606
Total RNA
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX190848
https://www.ncbi.nlm.nih.gov/biosample/SAMN01737708
1
cell line: HL60,rna fraction: Non-polyadenylated RNA
Craig L. Dobbin Genetics Research Centre,
St. John's
Canada
Memorial University of Newfoundland
Touati,,Benoukraf
Bases were called using Casava 1.8.4 with default settings.,76-bp paired-end reads were aligned to human genome (hg19) using tophat 2.0.2 with default settings and without a reference assembly.,Assemblies were generated using Cufflinks 2.0.2 again, without reference assembly,Overlap with DNMT1-RIP-Seq was calculated using Bedtools.,Genome_build: hg19,Supplementary_files_format_and_content: Whole-transcriptome .gtf assemblies of Total and polyA(-) RNA samples, including FPKM values.
Total RNA was extracted with TRI REAGENT® (MRC). Total RNA was extracted with TRI Reagent® (MRC). RNA samples were treated with DNase I (10 U of DNase I (Roche) per 3 ug of total RNA; 37ºC for one hour; in the presence of RNase inhibitor). Non-polyadenylated RNA fractions were selected with the MicroPoly (A) PuristTM purification kit (Ambion). Total and not-polyadenylated RNA were depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit (cat. # MRZG126 Epicentre).,Double stranded cDNA libraries were constructed using ScriptSeq™ v2 RNA-Seq Library Preparation Kit (cat. # SSV21106 Epicentre) followed by Duplex Specific Nuclease (DSN) normalization (Evrogen, EA001). DSN treated libraries were subjected to final size-selection in 3% agarose gel. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). Libraries were sequenced (1/lane) on a HiSeq 2000 Illumina instrument.
GSM1013481
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX190849,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01737709
GSM1013481
GSE32260,GSE41279
0.034869
Myeloid Leukemia
Public on Dec 01 2012
Oct 02 2012
9606
Total RNA polyA(-)
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX190849
https://www.ncbi.nlm.nih.gov/biosample/SAMN01737709
1
cell line: HT29,cell type: colon cancer,treatment: control
Stony Brook University
Stony Brook
USA
Stony Brook University BME
Xiao,,Xu
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated to represent gene expression intensities,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols
GSM1019735
Illumina HiSeq 2000
Aug 08 2023
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195293,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765636
GSM1019735
GSE41586,GSE41588
0
HT29 treated with 0 μM of 5-Aza
Public on Sep 17 2013
Oct 15 2012
9606
HT29 at 0 μM of 5-Aza, biological rep1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX195293
https://www.ncbi.nlm.nih.gov/biosample/SAMN01765636
1
cell line: HT29,cell type: colon cancer,treatment: control
Stony Brook University
Stony Brook
USA
Stony Brook University BME
Xiao,,Xu
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated to represent gene expression intensities,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols
GSM1019736
Illumina HiSeq 2000
Aug 08 2023
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195294,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765637
GSM1019736
GSE41586,GSE41588
0
HT29 treated with 0 μM of 5-Aza
Public on Sep 17 2013
Oct 15 2012
9606
HT29 at 0 μM of 5-Aza, biological rep2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX195294
https://www.ncbi.nlm.nih.gov/biosample/SAMN01765637
1
cell line: HT29,cell type: colon cancer,treatment: control
Stony Brook University
Stony Brook
USA
Stony Brook University BME
Xiao,,Xu
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated to represent gene expression intensities,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols
GSM1019737
Illumina HiSeq 2000
Aug 08 2023
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195295,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765638
GSM1019737
GSE41586,GSE41588
0
HT29 treated with 0 μM of 5-Aza
Public on Sep 17 2013
Oct 15 2012
9606
HT29 at 0 μM of 5-Aza, biological rep3
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX195295
https://www.ncbi.nlm.nih.gov/biosample/SAMN01765638
1
cell line: HT29,cell type: colon cancer,treatment: 5-Aza low
Stony Brook University
Stony Brook
USA
Stony Brook University BME
Xiao,,Xu
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated to represent gene expression intensities,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols
GSM1019738
Illumina HiSeq 2000
Aug 08 2023
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195296,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765639
GSM1019738
GSE41586,GSE41588
0.001323
HT29 treated with 5 μM of 5-Aza
Public on Sep 17 2013
Oct 15 2012
9606
HT29 at 5 μM of 5-Aza, biological rep1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX195296
https://www.ncbi.nlm.nih.gov/biosample/SAMN01765639
1
cell line: HT29,cell type: colon cancer,treatment: 5-Aza low
Stony Brook University
Stony Brook
USA
Stony Brook University BME
Xiao,,Xu
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated to represent gene expression intensities,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols
GSM1019739
Illumina HiSeq 2000
Aug 08 2023
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195297,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765640
GSM1019739
GSE41586,GSE41588
0.00094
HT29 treated with 5 μM of 5-Aza
Public on Sep 17 2013
Oct 15 2012
9606
HT29 at 5 μM of 5-Aza, biological rep2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX195297
https://www.ncbi.nlm.nih.gov/biosample/SAMN01765640
1
cell line: HT29,cell type: colon cancer,treatment: 5-Aza low
Stony Brook University
Stony Brook
USA
Stony Brook University BME
Xiao,,Xu
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated to represent gene expression intensities,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols
GSM1019740
Illumina HiSeq 2000
Aug 08 2023
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195298,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765641
GSM1019740
GSE41586,GSE41588
0.001323
HT29 treated with 5 μM of 5-Aza
Public on Sep 17 2013
Oct 15 2012
9606
HT29 at 5 μM of 5-Aza, biological rep3
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX195298
https://www.ncbi.nlm.nih.gov/biosample/SAMN01765641
1
cell line: HT29,cell type: colon cancer,treatment: 5-Aza high
Stony Brook University
Stony Brook
USA
Stony Brook University BME
Xiao,,Xu
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated to represent gene expression intensities,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols
GSM1019741
Illumina HiSeq 2000
Aug 08 2023
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195299,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765642
GSM1019741
GSE41586,GSE41588
0
HT29 treated with 10 μM of 5-Aza
Public on Sep 17 2013
Oct 15 2012
9606
HT29 at 10 μM of 5-Aza, biological rep1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX195299
https://www.ncbi.nlm.nih.gov/biosample/SAMN01765642
1
cell line: HT29,cell type: colon cancer,treatment: 5-Aza high
Stony Brook University
Stony Brook
USA
Stony Brook University BME
Xiao,,Xu
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated to represent gene expression intensities,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols
GSM1019742
Illumina HiSeq 2000
Aug 08 2023
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195300,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765643
GSM1019742
GSE41586,GSE41588
0.000149
HT29 treated with 10 μM of 5-Aza
Public on Sep 17 2013
Oct 15 2012
9606
HT29 at 10 μM of 5-Aza, biological rep2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX195300
https://www.ncbi.nlm.nih.gov/biosample/SAMN01765643
1
cell line: HT29,cell type: colon cancer,treatment: 5-Aza high
Stony Brook University
Stony Brook
USA
Stony Brook University BME
Xiao,,Xu
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence and low quality bases (first 3 bases), then mapped to hg19 whole genome using tophatv 2.0.1 with parameters -r 10 -p 4,mapped reads from tophat were further quantifiled through Cufflink program (version 1.3.0),Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated to represent gene expression intensities,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.,Paired end 100 bp RNA-Seq libraries were prepared for sequencing using standard Illumina protocols
GSM1019743
Illumina HiSeq 2000
Aug 08 2023
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195301,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01765644
GSM1019743
GSE41586,GSE41588
0.00431
HT29 treated with 10 μM of 5-Aza
Public on Sep 17 2013
Oct 15 2012
9606
HT29 at 10 μM of 5-Aza, biological rep3
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX195301
https://www.ncbi.nlm.nih.gov/biosample/SAMN01765644
1
cell type: corneal endothelial cells,age: 31y
Gonda BLDG Rm. 6554, P.O.Box 957088
Los Angeles
USA
UCLA
Kevin,,Huang
each sample was subjected to sequencing according to manufacturer’s instruction with Illumina Hiseq 2000. Reads were mapped to the hg19 genome using BWA.,For all datasets analyzed, we first transformed transcript read counts to the RPKM metric, and genes with an average RPKM<1 were filtered out, followed by quantile normalization.,Genome_build: hg19,Supplementary_files_format_and_content: filtered and normalized RPKM table
RNA were extracted from those adult and fetal tissues using RNeasy Micro Kit (Qiagen, Cat. No. 74004, CA,USA). RNA concentration was detected by nanodrop spectrophotometer,RNA-Seq library construction followed the protocol described in illumina TruSeq™ RNA Sample Preparation Guide. Library construction was started with 100ng total RNA, via poly-T oligo-attached magnetic beads to purify the poly-A containing mRNA molecules. RNA fragments were reverse transcribed into first stand cDNA, follwed by synthesis second strand cDNA. After end repaired with a single ‘A’ base, cDNAs were ligated with different adapters for PCR amplification. After amplified for 15 cycles, the concentration of product was tested by the Qubit Fluorometer (Invitrogen, USA).
GSM1020212
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
Reanalyzed by: GSE81474,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195461,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01766527
GSM1020212
GSE41616
0.004722
corneal endothelial cells
Public on Jan 08 2013
Oct 16 2012
9606
adult CEC 33
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX195461
https://www.ncbi.nlm.nih.gov/biosample/SAMN01766527
1
cell type: corneal endothelial cells,age: 56y
Gonda BLDG Rm. 6554, P.O.Box 957088
Los Angeles
USA
UCLA
Kevin,,Huang
each sample was subjected to sequencing according to manufacturer’s instruction with Illumina Hiseq 2000. Reads were mapped to the hg19 genome using BWA.,For all datasets analyzed, we first transformed transcript read counts to the RPKM metric, and genes with an average RPKM<1 were filtered out, followed by quantile normalization.,Genome_build: hg19,Supplementary_files_format_and_content: filtered and normalized RPKM table
RNA were extracted from those adult and fetal tissues using RNeasy Micro Kit (Qiagen, Cat. No. 74004, CA,USA). RNA concentration was detected by nanodrop spectrophotometer,RNA-Seq library construction followed the protocol described in illumina TruSeq™ RNA Sample Preparation Guide. Library construction was started with 100ng total RNA, via poly-T oligo-attached magnetic beads to purify the poly-A containing mRNA molecules. RNA fragments were reverse transcribed into first stand cDNA, follwed by synthesis second strand cDNA. After end repaired with a single ‘A’ base, cDNAs were ligated with different adapters for PCR amplification. After amplified for 15 cycles, the concentration of product was tested by the Qubit Fluorometer (Invitrogen, USA).
GSM1020213
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
Reanalyzed by: GSE81474,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195462,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01766528
GSM1020213
GSE41616
0.007024
corneal endothelial cells
Public on Jan 08 2013
Oct 16 2012
9606
adult CEC 39
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX195462
https://www.ncbi.nlm.nih.gov/biosample/SAMN01766528
1
cell type: corneal endothelial cells,age: 64y
Gonda BLDG Rm. 6554, P.O.Box 957088
Los Angeles
USA
UCLA
Kevin,,Huang
each sample was subjected to sequencing according to manufacturer’s instruction with Illumina Hiseq 2000. Reads were mapped to the hg19 genome using BWA.,For all datasets analyzed, we first transformed transcript read counts to the RPKM metric, and genes with an average RPKM<1 were filtered out, followed by quantile normalization.,Genome_build: hg19,Supplementary_files_format_and_content: filtered and normalized RPKM table
RNA were extracted from those adult and fetal tissues using RNeasy Micro Kit (Qiagen, Cat. No. 74004, CA,USA). RNA concentration was detected by nanodrop spectrophotometer,RNA-Seq library construction followed the protocol described in illumina TruSeq™ RNA Sample Preparation Guide. Library construction was started with 100ng total RNA, via poly-T oligo-attached magnetic beads to purify the poly-A containing mRNA molecules. RNA fragments were reverse transcribed into first stand cDNA, follwed by synthesis second strand cDNA. After end repaired with a single ‘A’ base, cDNAs were ligated with different adapters for PCR amplification. After amplified for 15 cycles, the concentration of product was tested by the Qubit Fluorometer (Invitrogen, USA).
GSM1020214
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
Reanalyzed by: GSE81474,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195463,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01766529
GSM1020214
GSE41616
0
corneal endothelial cells
Public on Jan 08 2013
Oct 16 2012
9606
adult CEC 40
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX195463
https://www.ncbi.nlm.nih.gov/biosample/SAMN01766529
1
cell type: corneal endothelial cells,age: gestation age 16-18wk
Gonda BLDG Rm. 6554, P.O.Box 957088
Los Angeles
USA
UCLA
Kevin,,Huang
each sample was subjected to sequencing according to manufacturer’s instruction with Illumina Hiseq 2000. Reads were mapped to the hg19 genome using BWA.,For all datasets analyzed, we first transformed transcript read counts to the RPKM metric, and genes with an average RPKM<1 were filtered out, followed by quantile normalization.,Genome_build: hg19,Supplementary_files_format_and_content: filtered and normalized RPKM table
RNA were extracted from those adult and fetal tissues using RNeasy Micro Kit (Qiagen, Cat. No. 74004, CA,USA). RNA concentration was detected by nanodrop spectrophotometer,RNA-Seq library construction followed the protocol described in illumina TruSeq™ RNA Sample Preparation Guide. Library construction was started with 100ng total RNA, via poly-T oligo-attached magnetic beads to purify the poly-A containing mRNA molecules. RNA fragments were reverse transcribed into first stand cDNA, follwed by synthesis second strand cDNA. After end repaired with a single ‘A’ base, cDNAs were ligated with different adapters for PCR amplification. After amplified for 15 cycles, the concentration of product was tested by the Qubit Fluorometer (Invitrogen, USA).
GSM1020215
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
Reanalyzed by: GSE81474,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195464,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01766530
GSM1020215
GSE41616
0.006755
corneal endothelial cells
Public on Jan 08 2013
Oct 16 2012
9606
fetal CEC 1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX195464
https://www.ncbi.nlm.nih.gov/biosample/SAMN01766530
1
cell type: corneal endothelial cells,age: gestation age 16-18wk
Gonda BLDG Rm. 6554, P.O.Box 957088
Los Angeles
USA
UCLA
Kevin,,Huang
each sample was subjected to sequencing according to manufacturer’s instruction with Illumina Hiseq 2000. Reads were mapped to the hg19 genome using BWA.,For all datasets analyzed, we first transformed transcript read counts to the RPKM metric, and genes with an average RPKM<1 were filtered out, followed by quantile normalization.,Genome_build: hg19,Supplementary_files_format_and_content: filtered and normalized RPKM table
RNA were extracted from those adult and fetal tissues using RNeasy Micro Kit (Qiagen, Cat. No. 74004, CA,USA). RNA concentration was detected by nanodrop spectrophotometer,RNA-Seq library construction followed the protocol described in illumina TruSeq™ RNA Sample Preparation Guide. Library construction was started with 100ng total RNA, via poly-T oligo-attached magnetic beads to purify the poly-A containing mRNA molecules. RNA fragments were reverse transcribed into first stand cDNA, follwed by synthesis second strand cDNA. After end repaired with a single ‘A’ base, cDNAs were ligated with different adapters for PCR amplification. After amplified for 15 cycles, the concentration of product was tested by the Qubit Fluorometer (Invitrogen, USA).
GSM1020216
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
Reanalyzed by: GSE81474,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX195465,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01766531
GSM1020216
GSE41616
0.074061
corneal endothelial cells
Public on Jan 08 2013
Oct 16 2012
9606
fetal CEC 2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX195465
https://www.ncbi.nlm.nih.gov/biosample/SAMN01766531
1
passage number: 5,cell type: fibroblast
230 South Frontage Road
New Haven
USA
Yale University
Flora,,Vaccarino
Base calling: Illumina CASAVA,Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data],Conversion from BAM to SAM: SAMtools 0.1.11,Conversion SAM to MRF: sam2mrf (part of RSEQtools, couldn't find RSEQtools version, it is whatever version was available as of August 2011),RPKM computation: mrfQuantifier (part of RSEQtools, same note about version),Genome_build: hGRC37 (hg19)
Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).,Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare as well using standard Illumina protocols using 2.5 ug of total RNA. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2.5 ug of total RNA for the construction of multiplex sequencing libraries for all iPSC for members of family S1123. In all cases, library fragments of ~300 bp were band isolated from an agarose gel.
GSM1023063
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX198056,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01773270
GSM1023063
GSE41716
0.002273
fibroblast
Public on Oct 31 2012
Oct 19 2012
9606
RNA 03-02, F
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX198056
https://www.ncbi.nlm.nih.gov/biosample/SAMN01773270
1
passage number: 8,cell type: iPS
230 South Frontage Road
New Haven
USA
Yale University
Flora,,Vaccarino
Base calling: Illumina CASAVA,Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data],Conversion from BAM to SAM: SAMtools 0.1.11,Conversion SAM to MRF: sam2mrf (part of RSEQtools, couldn't find RSEQtools version, it is whatever version was available as of August 2011),RPKM computation: mrfQuantifier (part of RSEQtools, same note about version),Genome_build: hGRC37 (hg19)
Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).,Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare as well using standard Illumina protocols using 2.5 ug of total RNA. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2.5 ug of total RNA for the construction of multiplex sequencing libraries for all iPSC for members of family S1123. In all cases, library fragments of ~300 bp were band isolated from an agarose gel.
GSM1023076
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX198069,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01773283
GSM1023076
GSE41716
0.019931
iPS
Public on Oct 31 2012
Oct 19 2012
9606
RNA S1123-01, i1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX198069
https://www.ncbi.nlm.nih.gov/biosample/SAMN01773283
1
passage number: 7,cell type: iPS
230 South Frontage Road
New Haven
USA
Yale University
Flora,,Vaccarino
Base calling: Illumina CASAVA,Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data],Conversion from BAM to SAM: SAMtools 0.1.11,Conversion SAM to MRF: sam2mrf (part of RSEQtools, couldn't find RSEQtools version, it is whatever version was available as of August 2011),RPKM computation: mrfQuantifier (part of RSEQtools, same note about version),Genome_build: hGRC37 (hg19)
Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).,Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare as well using standard Illumina protocols using 2.5 ug of total RNA. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2.5 ug of total RNA for the construction of multiplex sequencing libraries for all iPSC for members of family S1123. In all cases, library fragments of ~300 bp were band isolated from an agarose gel.
GSM1023077
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX198070,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01773284
GSM1023077
GSE41716
0.011621
iPS
Public on Oct 31 2012
Oct 19 2012
9606
RNA S1123-01, i3
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX198070
https://www.ncbi.nlm.nih.gov/biosample/SAMN01773284
1
passage number: 8,cell type: iPS
230 South Frontage Road
New Haven
USA
Yale University
Flora,,Vaccarino
Base calling: Illumina CASAVA,Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data],Conversion from BAM to SAM: SAMtools 0.1.11,Conversion SAM to MRF: sam2mrf (part of RSEQtools, couldn't find RSEQtools version, it is whatever version was available as of August 2011),RPKM computation: mrfQuantifier (part of RSEQtools, same note about version),Genome_build: hGRC37 (hg19)
Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).,Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare as well using standard Illumina protocols using 2.5 ug of total RNA. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2.5 ug of total RNA for the construction of multiplex sequencing libraries for all iPSC for members of family S1123. In all cases, library fragments of ~300 bp were band isolated from an agarose gel.
GSM1023078
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX198071,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01773285
GSM1023078
GSE41716
0.016357
iPS
Public on Oct 31 2012
Oct 19 2012
9606
RNA S1123-01, i4
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX198071
https://www.ncbi.nlm.nih.gov/biosample/SAMN01773285
1
passage number: 6,cell type: iPS
230 South Frontage Road
New Haven
USA
Yale University
Flora,,Vaccarino
Base calling: Illumina CASAVA,Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data],Conversion from BAM to SAM: SAMtools 0.1.11,Conversion SAM to MRF: sam2mrf (part of RSEQtools, couldn't find RSEQtools version, it is whatever version was available as of August 2011),RPKM computation: mrfQuantifier (part of RSEQtools, same note about version),Genome_build: hGRC37 (hg19)
Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).,Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare as well using standard Illumina protocols using 2.5 ug of total RNA. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2.5 ug of total RNA for the construction of multiplex sequencing libraries for all iPSC for members of family S1123. In all cases, library fragments of ~300 bp were band isolated from an agarose gel.
GSM1023080
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX198073,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01773287
GSM1023080
GSE41716
0.023139
iPS
Public on Oct 31 2012
Oct 19 2012
9606
RNA S1123-02, i11
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX198073
https://www.ncbi.nlm.nih.gov/biosample/SAMN01773287
1
passage number: 6,cell type: iPS
230 South Frontage Road
New Haven
USA
Yale University
Flora,,Vaccarino
Base calling: Illumina CASAVA,Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data],Conversion from BAM to SAM: SAMtools 0.1.11,Conversion SAM to MRF: sam2mrf (part of RSEQtools, couldn't find RSEQtools version, it is whatever version was available as of August 2011),RPKM computation: mrfQuantifier (part of RSEQtools, same note about version),Genome_build: hGRC37 (hg19)
Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).,Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare as well using standard Illumina protocols using 2.5 ug of total RNA. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2.5 ug of total RNA for the construction of multiplex sequencing libraries for all iPSC for members of family S1123. In all cases, library fragments of ~300 bp were band isolated from an agarose gel.
GSM1023081
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX198074,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01773288
GSM1023081
GSE41716
0.032279
iPS
Public on Oct 31 2012
Oct 19 2012
9606
RNA S1123-02, i17
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX198074
https://www.ncbi.nlm.nih.gov/biosample/SAMN01773288
1
passage number: 9,cell type: iPS
230 South Frontage Road
New Haven
USA
Yale University
Flora,,Vaccarino
Base calling: Illumina CASAVA,Alignment: Tophat 1.3.1, parameters --solexa1.3-quals --coverage-search --no-novel-indels --microexon-search [extra parameter "-r 100" for PE 2x100 data, "-r 150" for 2x75 data and without "-r" parameter for SE data],Conversion from BAM to SAM: SAMtools 0.1.11,Conversion SAM to MRF: sam2mrf (part of RSEQtools, couldn't find RSEQtools version, it is whatever version was available as of August 2011),RPKM computation: mrfQuantifier (part of RSEQtools, same note about version),Genome_build: hGRC37 (hg19)
Cells were treated with Accutase and pelleted. Total RNA was extracted using PicoPure kit (Life Technologies catalog # KIT0204).,Fibroblast RNA libraries for both families (03 and 1123) were prepared for sequencing using standard Illumina protocols using 5 ug of total RNA. iPSC RNA libraries for family 03 were prepare as well using standard Illumina protocols using 2.5 ug of total RNA. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2.5 ug of total RNA for the construction of multiplex sequencing libraries for all iPSC for members of family S1123. In all cases, library fragments of ~300 bp were band isolated from an agarose gel.
GSM1023082
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX198075,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01773289
GSM1023082
GSE41716
0.021789
iPS
Public on Oct 31 2012
Oct 19 2012
9606
RNA S1123-02, i2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX198075
https://www.ncbi.nlm.nih.gov/biosample/SAMN01773289
1
strain: HUES 3Hb9::GFP,day of collection: Day 21 GFP high,treatment: SHH derived,cell type: FACS-purified motor neurons
52 Oxford St.
Cambridge
USA
Harvard University
Mackenzie,W.,Amoroso
The RNA samples sequenced on an Illumina HiSeq instrument at the HudsonAlpha Institute of Biotechnology.,The reads were aligned to the reference transcriptome as well as a library of exon junctions using Bowtie,Data was analyzed using Expression Plot using a P value of 0.0001 and a 2 fold change threshold,Gene ontology was performed using DAVID with enrichment sets from Expression Plot.
Trizol extraction of total RNA,NuGEN RNA kit for genomic sample amplification
GSM1024416
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX200689,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01779691
GSM1024416
GSE41795
0.070256
Human Stem Derived Motor Neurons GFP high
Public on Feb 06 2013
Oct 23 2012
9606
Positive Sample 1 SL16147
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX200689
https://www.ncbi.nlm.nih.gov/biosample/SAMN01779691
1
strain: HUES 3Hb9::GFP,day of collection: Day 21 GFP high,treatment: S+P derived,cell type: FACS-purified motor neurons
52 Oxford St.
Cambridge
USA
Harvard University
Mackenzie,W.,Amoroso
The RNA samples sequenced on an Illumina HiSeq instrument at the HudsonAlpha Institute of Biotechnology.,The reads were aligned to the reference transcriptome as well as a library of exon junctions using Bowtie,Data was analyzed using Expression Plot using a P value of 0.0001 and a 2 fold change threshold,Gene ontology was performed using DAVID with enrichment sets from Expression Plot.
Trizol extraction of total RNA,NuGEN RNA kit for genomic sample amplification
GSM1024417
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX200690,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01779692
GSM1024417
GSE41795
0.128037
Human Stem Derived Motor Neurons GFP high
Public on Feb 06 2013
Oct 23 2012
9606
Positive Sample 2 SL16145
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX200690
https://www.ncbi.nlm.nih.gov/biosample/SAMN01779692
1
strain: HUES 3Hb9::GFP,day of collection: Day 21 no GFP,treatment: S+P derived,cell type: FACS-purified motor neurons
52 Oxford St.
Cambridge
USA
Harvard University
Mackenzie,W.,Amoroso
The RNA samples sequenced on an Illumina HiSeq instrument at the HudsonAlpha Institute of Biotechnology.,The reads were aligned to the reference transcriptome as well as a library of exon junctions using Bowtie,Data was analyzed using Expression Plot using a P value of 0.0001 and a 2 fold change threshold,Gene ontology was performed using DAVID with enrichment sets from Expression Plot.
Trizol extraction of total RNA,NuGEN RNA kit for genomic sample amplification
GSM1024418
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX200691,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01779693
GSM1024418
GSE41795
0.021962
Human Stem Derived Motor Neurons no GFP
Public on Feb 06 2013
Oct 23 2012
9606
Negative Sample 1 SL16148
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX200691
https://www.ncbi.nlm.nih.gov/biosample/SAMN01779693
1
cell line: BJ cells,condition: Proliferation, normal conditions
Ramat Aviv
Tel Aviv
Israel
Tel Aviv University
Ran,,Elkon
Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Genome build: hg19,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads
Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions.
GSM1041191
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX207917,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01821792
GSM1041191
GSE42509,GSE45833
0.003462
Immortalized primary fibroblasts
Public on Mar 24 2013
Nov 26 2012
9606
C1.rna
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX207917
https://www.ncbi.nlm.nih.gov/biosample/SAMN01821792
1
cell line: BJ cells,condition: Proliferation, normal conditions
Ramat Aviv
Tel Aviv
Israel
Tel Aviv University
Ran,,Elkon
Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Genome build: hg19,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads
Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions.
GSM1041192
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX207918,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01821793
GSM1041192
GSE42509,GSE45833
0.004334
Immortalized primary fibroblasts
Public on Mar 24 2013
Nov 26 2012
9606
C2.rna
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX207918
https://www.ncbi.nlm.nih.gov/biosample/SAMN01821793
1
cell line: BJ cells,condition: Quiescence induced by serum depletion
Ramat Aviv
Tel Aviv
Israel
Tel Aviv University
Ran,,Elkon
Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Genome build: hg19,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads
Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions.
GSM1041193
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX207919,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01821794
GSM1041193
GSE42509,GSE45833
0.008406
Immortalized primary fibroblasts
Public on Mar 24 2013
Nov 26 2012
9606
Q1.rna
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX207919
https://www.ncbi.nlm.nih.gov/biosample/SAMN01821794
1
cell line: BJ cells,condition: Quiescence induced by serum depletion
Ramat Aviv
Tel Aviv
Israel
Tel Aviv University
Ran,,Elkon
Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Genome build: hg19,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads
Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions.
GSM1041194
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX207920,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01821795
GSM1041194
GSE42509,GSE45833
0.003264
Immortalized primary fibroblasts
Public on Mar 24 2013
Nov 26 2012
9606
Q2.rna
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX207920
https://www.ncbi.nlm.nih.gov/biosample/SAMN01821795
1
cell line: BJ cells,condition: pre-senescence; 5 dys after RASG12V induction,protocol: BJ cells expressing hTERT and tamoxifen-inducible RASG12V were cultured in the presence of 10-7M 4-OHT-Tamoxifen for 5 days
Ramat Aviv
Tel Aviv
Israel
Tel Aviv University
Ran,,Elkon
Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Genome build: hg19,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads
Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions.
GSM1041195
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX207921,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01821796
GSM1041195
GSE42509,GSE45833
0.003264
Immortalized primary fibroblasts
Public on Mar 24 2013
Nov 26 2012
9606
preS1.rna
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX207921
https://www.ncbi.nlm.nih.gov/biosample/SAMN01821796
1
cell line: BJ cells,condition: pre-senescence; 5 dys after RASG12V induction,protocol: BJ cells expressing hTERT and tamoxifen-inducible RASG12V were cultured in the presence of 10-7M 4-OHT-Tamoxifen for 5 days
Ramat Aviv
Tel Aviv
Israel
Tel Aviv University
Ran,,Elkon
Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Genome build: hg19,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads
Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen). Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions.
GSM1041196
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX207922,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01821797
GSM1041196
GSE42509,GSE45833
0.002747
Immortalized primary fibroblasts
Public on Mar 24 2013
Nov 26 2012
9606
preS2.rna
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX207922
https://www.ncbi.nlm.nih.gov/biosample/SAMN01821797
1
cell type: NTera2/D1,treatment: none
9500 Gilman Drive
La Jolla
USA
HHMI/UCSD
MICHAEL,G,ROSENFELD
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.,The sequencing reads were aligned to hg18 using BFAST, and we kept only 1 aligned read/ genome position for downstream analyses.,An equal number of reads (4.4 million) was randomly extracted from each sample, and the sequencing reads were counted over the entire gene body on the sense strand with respect to the gene orientation using BedTools.,Genome_build: hg18,Supplementary_files_format_and_content: BED aligned files and BEDGRAPH files
After harvesting the cells, RNA polymerases were allowed to run-on for 5 minutes at 30C (~100bp) in the presence of sarkosyl and BrUTP. The RNA was then base hydrolyzed and purified. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads. Run-on RNA was then polyadenylated to generate primer sites for first strand cDNA synthesis. Complementary poly-T primers contain two adaptor sequences separated by an Ape1 restriction site, which after circularization and Ape1 digestion, will terminate both ends, thus permitting cDNA generation, PCR-amplification, and library generation for deep sequencing.
GSM1045177
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX206683,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01820058
GSM1045177
GSE42563,GSE42602
0.123891
NTera2/D1 cells
Public on Dec 29 2012
Nov 27 2012
9606
minusRA_GRO-seq
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX206683
https://www.ncbi.nlm.nih.gov/biosample/SAMN01820058
1
cell type: gastric adenocarcinoma cells,cell line: BGC-823
No.7 PengFei road
Shenzhen
China
Agricultural Genomes Institute at Shenzhen
Desheng,,Gong
Illumina BclConverter-1.9.0 software used for basecalling.,Adaptor sequences were removed, and low-quality sequence reads were trimmed. The clean reads of RNA sequencing reads were aligned to the reference genome (UCSC hg18) using the SOAP aligner with parameters -m 90 -x 500 -l 15 -s 35 -p 4,Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.,Genome_build: hg18,Supplementary_files_format_and_content: bed files: contained chromsome,reads strart site,reads end sites;tab-delimited text files include RPKM values for each Sample
Total RNA was isolated from BGC-823, AGS cells and YH cells using the miRNeasy Kit (Qiagen 74104) according to the manufacturer's protocol. An additional DNaseI digestion step was performed to ensure that the samples were not contaminated with genomic DNA. The RNA purity was assessed using the Agilent bioanalyzer. Total RNA was converted to cDNA using the NuGEN Ovation RNA-Seq System according to the manufacturer's protocol (NuGEN, San Carlos, CA, USA). The cDNA was then used for Illumina sequencing library preparation. DNA fragments were end-repaired to generate blunt ends with 5′ phosphatase and 3′ hydroxyls, and adapters were ligated for paired-end sequencing on an Illumina HiSeq 2000.
GSM1056529
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX212298,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01840352
GSM1056529
GSE43093,GSE43096
0
gastric adenocarcinoma cells
Public on Jul 01 2014
Dec 21 2012
9606
BGC-823-RNA-seq
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX212298
https://www.ncbi.nlm.nih.gov/biosample/SAMN01840352
1
cell line: CNE1,cell type: human nasopharyngeal carcinoma cells,passages: 3,infected with: control lentivirus
Southern medical university
Guangzhou
China
Southern medical university
Xin,,Li
The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.,To get the clean reads, removing the dirty raw reads is needed before data analysis. Filter steps: 1. Remove reads with adaptors; 2. Remove reads in which unknown bases are more than 10%; 3. Remove low quality reads (the percentage of the low quality bases of quality value <5 is more than 50% in a read),Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.,Genome_build: hg19,Supplementary_files_format_and_content: RPKM values for each Sample .
Total RNA isolated with TRIzol reagent was treated with RNase-free DNase (NEB) at 37 oC for 10 minutes. The Dynabeads mRNA Purification Kit (Life Technologies) was used to isolate mRNA from the total RNA samples.,According to the manufacturer’s instructions, the mRNA was chemically fragmented by the use of divalent cations and converted into single-stranded cDNA using random hexamer primers and SuperscriptⅡ reverse transcriptase (Life Technologies). The second strand was generated to create double-stranded cDNA using RNase H (Enzymatics) and DNA polymerase. The cDNA products was purified by Ampure beads XP (Beckman).After converting the overhangs into blunt ends using T4 DNA polymerase and Klenow DNA polymerase, an ‘A’ base was added to the 3’ end of the DNA fragments by the polymerase activity of Klenow fragment. Sequencing adapters were subsequently ligated to the ends of the cDNA fragments using T4 DNA Ligase (Enzymatics). The fragments of 200bp were selected by Ampure beads XP (Beckman) and enriched by 12 cycles of PCR. The PCR products were loaded into flowcell to generate clusters and then sequenced by Hiseq 2000 (Illumina).
GSM1057039
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX212471,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01853566
GSM1057039
GSE42945,GSE43126
0
CNE1-MOCK_RNA-seq
Public on Jun 30 2015
Dec 22 2012
9606
CNE1-MOCK
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX212471
https://www.ncbi.nlm.nih.gov/biosample/SAMN01853566
1
cell line: CNE1,cell type: human nasopharyngeal carcinoma cells,passages: 3,infected with: EBV-miRNA-BART1 lentivirus
Southern medical university
Guangzhou
China
Southern medical university
Xin,,Li
The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.,To get the clean reads, removing the dirty raw reads is needed before data analysis. Filter steps: 1. Remove reads with adaptors; 2. Remove reads in which unknown bases are more than 10%; 3. Remove low quality reads (the percentage of the low quality bases of quality value <5 is more than 50% in a read),Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.,Genome_build: hg19,Supplementary_files_format_and_content: RPKM values for each Sample .
Total RNA isolated with TRIzol reagent was treated with RNase-free DNase (NEB) at 37 oC for 10 minutes. The Dynabeads mRNA Purification Kit (Life Technologies) was used to isolate mRNA from the total RNA samples.,According to the manufacturer’s instructions, the mRNA was chemically fragmented by the use of divalent cations and converted into single-stranded cDNA using random hexamer primers and SuperscriptⅡ reverse transcriptase (Life Technologies). The second strand was generated to create double-stranded cDNA using RNase H (Enzymatics) and DNA polymerase. The cDNA products was purified by Ampure beads XP (Beckman).After converting the overhangs into blunt ends using T4 DNA polymerase and Klenow DNA polymerase, an ‘A’ base was added to the 3’ end of the DNA fragments by the polymerase activity of Klenow fragment. Sequencing adapters were subsequently ligated to the ends of the cDNA fragments using T4 DNA Ligase (Enzymatics). The fragments of 200bp were selected by Ampure beads XP (Beckman) and enriched by 12 cycles of PCR. The PCR products were loaded into flowcell to generate clusters and then sequenced by Hiseq 2000 (Illumina).
GSM1057040
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX212472,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01853567
GSM1057040
GSE42945,GSE43126
0
CNE1-BART1_RNA-seq
Public on Jun 30 2015
Dec 22 2012
9606
CNE1-BART1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX212472
https://www.ncbi.nlm.nih.gov/biosample/SAMN01853567
1
cell line: CNE1,cell type: human nasopharyngeal carcinoma cells,passages: 3,infected with: EBV-miRNA-BART3 lentivirus
Southern medical university
Guangzhou
China
Southern medical university
Xin,,Li
The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.,To get the clean reads, removing the dirty raw reads is needed before data analysis. Filter steps: 1. Remove reads with adaptors; 2. Remove reads in which unknown bases are more than 10%; 3. Remove low quality reads (the percentage of the low quality bases of quality value <5 is more than 50% in a read),Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.,Genome_build: hg19,Supplementary_files_format_and_content: RPKM values for each Sample .
Total RNA isolated with TRIzol reagent was treated with RNase-free DNase (NEB) at 37 oC for 10 minutes. The Dynabeads mRNA Purification Kit (Life Technologies) was used to isolate mRNA from the total RNA samples.,According to the manufacturer’s instructions, the mRNA was chemically fragmented by the use of divalent cations and converted into single-stranded cDNA using random hexamer primers and SuperscriptⅡ reverse transcriptase (Life Technologies). The second strand was generated to create double-stranded cDNA using RNase H (Enzymatics) and DNA polymerase. The cDNA products was purified by Ampure beads XP (Beckman).After converting the overhangs into blunt ends using T4 DNA polymerase and Klenow DNA polymerase, an ‘A’ base was added to the 3’ end of the DNA fragments by the polymerase activity of Klenow fragment. Sequencing adapters were subsequently ligated to the ends of the cDNA fragments using T4 DNA Ligase (Enzymatics). The fragments of 200bp were selected by Ampure beads XP (Beckman) and enriched by 12 cycles of PCR. The PCR products were loaded into flowcell to generate clusters and then sequenced by Hiseq 2000 (Illumina).
GSM1057041
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX212473,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01853568
GSM1057041
GSE42945,GSE43126
0
CNE1-BART3_RNA-seq
Public on Jun 30 2015
Dec 22 2012
9606
CNE1-BART3
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX212473
https://www.ncbi.nlm.nih.gov/biosample/SAMN01853568
1
cell line: CNE1,cell type: human nasopharyngeal carcinoma cells,passages: 3,infected with: EBV-miRNA-BART7 lentivirus
Southern medical university
Guangzhou
China
Southern medical university
Xin,,Li
The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.,To get the clean reads, removing the dirty raw reads is needed before data analysis. Filter steps: 1. Remove reads with adaptors; 2. Remove reads in which unknown bases are more than 10%; 3. Remove low quality reads (the percentage of the low quality bases of quality value <5 is more than 50% in a read),Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.,Genome_build: hg19,Supplementary_files_format_and_content: RPKM values for each Sample .
Total RNA isolated with TRIzol reagent was treated with RNase-free DNase (NEB) at 37 oC for 10 minutes. The Dynabeads mRNA Purification Kit (Life Technologies) was used to isolate mRNA from the total RNA samples.,According to the manufacturer’s instructions, the mRNA was chemically fragmented by the use of divalent cations and converted into single-stranded cDNA using random hexamer primers and SuperscriptⅡ reverse transcriptase (Life Technologies). The second strand was generated to create double-stranded cDNA using RNase H (Enzymatics) and DNA polymerase. The cDNA products was purified by Ampure beads XP (Beckman).After converting the overhangs into blunt ends using T4 DNA polymerase and Klenow DNA polymerase, an ‘A’ base was added to the 3’ end of the DNA fragments by the polymerase activity of Klenow fragment. Sequencing adapters were subsequently ligated to the ends of the cDNA fragments using T4 DNA Ligase (Enzymatics). The fragments of 200bp were selected by Ampure beads XP (Beckman) and enriched by 12 cycles of PCR. The PCR products were loaded into flowcell to generate clusters and then sequenced by Hiseq 2000 (Illumina).
GSM1057042
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX212474,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01853569
GSM1057042
GSE42945,GSE43126
0
CNE1-BART7_RNA-seq
Public on Jun 30 2015
Dec 22 2012
9606
CNE1-BART7
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX212474
https://www.ncbi.nlm.nih.gov/biosample/SAMN01853569
1
cell type: iPSC
1300 Morris Park Ave., F103
Bronx
USA
Albert Einstein College of Medicine
Herb,,Lachman
Illumina Casava1.7 software used for basecalling.,RNA-Seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 1.3.2 ),The resulting alignment data from Tophat were then fed to an assembler, Cufflinks (version 1.3.0) to assemble aligned RNA-Seq reads into transcripts,the program Cuffdiff was used to define differential expression,Genome_build: hg19,Supplementary_files_format_and_content: excel files include FPKM for each sample and some statistics
Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol. An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Each RNA sample had an A260:A280 ratio above 1.8, a RIN>9, and a A260:A230 ratio above 2.2. Briefly, total RNA was converted to cDNA, which was then used for Illumina sequencing library preparation.,RNA libraries were prepared for sequencing using standard Illumina protocols
GSM1057333
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX212595,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01860731
GSM1057333
GSE43143
0.016421
iPSC
Public on Jan 01 2014
Dec 26 2012
9606
tips_rna_seq
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX212595
https://www.ncbi.nlm.nih.gov/biosample/SAMN01860731
1
cell type: NPC
1300 Morris Park Ave., F103
Bronx
USA
Albert Einstein College of Medicine
Herb,,Lachman
Illumina Casava1.7 software used for basecalling.,RNA-Seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 1.3.2 ),The resulting alignment data from Tophat were then fed to an assembler, Cufflinks (version 1.3.0) to assemble aligned RNA-Seq reads into transcripts,the program Cuffdiff was used to define differential expression,Genome_build: hg19,Supplementary_files_format_and_content: excel files include FPKM for each sample and some statistics
Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturer’s protocol. An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Each RNA sample had an A260:A280 ratio above 1.8, a RIN>9, and a A260:A230 ratio above 2.2. Briefly, total RNA was converted to cDNA, which was then used for Illumina sequencing library preparation.,RNA libraries were prepared for sequencing using standard Illumina protocols
GSM1057334
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX212596,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01860732
GSM1057334
GSE43143
0.009923
NPC
Public on Jan 01 2014
Dec 26 2012
9606
NPC_rna_seq
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX212596
https://www.ncbi.nlm.nih.gov/biosample/SAMN01860732
1
cell line: MDA-MB-231,treatment: CXCL12 (0ng/mL) + IGF1 (0ng/mL)
417 East 68th Street
New York
USA
Memorial Sloan-Kettering Cancer Center
Xin,,Jin
Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, cells were harvested in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing libraries were constructed with 500ng polysome-associated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina).
GSM1060226
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215394,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883067
GSM1060226
GSE43296
0.003616
cells in culture
Public on Nov 01 2013
Jan 04 2013
9606
0+0_a
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX215394
https://www.ncbi.nlm.nih.gov/biosample/SAMN01883067
1
cell line: MDA-MB-231,treatment: CXCL12 (0ng/mL) + IGF1 (0ng/mL)
417 East 68th Street
New York
USA
Memorial Sloan-Kettering Cancer Center
Xin,,Jin
Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, cells were harvested in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing libraries were constructed with 500ng polysome-associated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina).
GSM1060227
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215395,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883068
GSM1060227
GSE43296
0.004891
cells in culture
Public on Nov 01 2013
Jan 04 2013
9606
0+0_b
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX215395
https://www.ncbi.nlm.nih.gov/biosample/SAMN01883068
1
cell line: MDA-MB-231,treatment: CXCL12 (30ng/mL) + IGF1 (10ng/mL)
417 East 68th Street
New York
USA
Memorial Sloan-Kettering Cancer Center
Xin,,Jin
Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, cells were harvested in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing libraries were constructed with 500ng polysome-associated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina).
GSM1060228
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215396,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883069
GSM1060228
GSE43296
0.022274
cells in culture
Public on Nov 01 2013
Jan 04 2013
9606
30+10_a
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX215396
https://www.ncbi.nlm.nih.gov/biosample/SAMN01883069
1
cell line: MDA-MB-231,treatment: CXCL12 (30ng/mL) + IGF1 (10ng/mL)
417 East 68th Street
New York
USA
Memorial Sloan-Kettering Cancer Center
Xin,,Jin
Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, cells were harvested in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing libraries were constructed with 500ng polysome-associated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina).
GSM1060229
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215397,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883070
GSM1060229
GSE43296
0.008008
cells in culture
Public on Nov 01 2013
Jan 04 2013
9606
30+10_b
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX215397
https://www.ncbi.nlm.nih.gov/biosample/SAMN01883070
1
cell line: MDA-MB-231,treatment: CXCL12 (300ng/mL) + IGF1 (100ng/mL)
417 East 68th Street
New York
USA
Memorial Sloan-Kettering Cancer Center
Xin,,Jin
Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, cells were harvested in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing libraries were constructed with 500ng polysome-associated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina).
GSM1060230
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215398,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883071
GSM1060230
GSE43296
0.021771
cells in culture
Public on Nov 01 2013
Jan 04 2013
9606
300+100_a
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX215398
https://www.ncbi.nlm.nih.gov/biosample/SAMN01883071
1
cell line: MDA-MB-231,treatment: CXCL12 (300ng/mL) + IGF1 (100ng/mL)
417 East 68th Street
New York
USA
Memorial Sloan-Kettering Cancer Center
Xin,,Jin
Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, cells were harvested in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing libraries were constructed with 500ng polysome-associated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina).
GSM1060231
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215399,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883072
GSM1060231
GSE43296
0.023018
cells in culture
Public on Nov 01 2013
Jan 04 2013
9606
300+100_b
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX215399
https://www.ncbi.nlm.nih.gov/biosample/SAMN01883072
1
cell line: EGFP-10a+ MDA-MB-231,protocol: supplemented with 1:1 ratio of MSC
417 East 68th Street
New York
USA
Memorial Sloan-Kettering Cancer Center
Xin,,Jin
Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, the whole tumor were harvested and cut into small pieces. Tumor slices were lysed in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing libraries were constructed with 500ng polysome-associated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina).
GSM1060352
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215400,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883073
GSM1060352
GSE43306
0.076879
mammary tumor xenograft
Public on Nov 01 2013
Jan 06 2013
9606
M1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX215400
https://www.ncbi.nlm.nih.gov/biosample/SAMN01883073
1
cell line: EGFP-10a+ MDA-MB-231,protocol: supplemented with 1:1 ratio of MSC
417 East 68th Street
New York
USA
Memorial Sloan-Kettering Cancer Center
Xin,,Jin
Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, the whole tumor were harvested and cut into small pieces. Tumor slices were lysed in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing libraries were constructed with 500ng polysome-associated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina).
GSM1060353
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215401,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883074
GSM1060353
GSE43306
0.005638
mammary tumor xenograft
Public on Nov 01 2013
Jan 06 2013
9606
M6
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX215401
https://www.ncbi.nlm.nih.gov/biosample/SAMN01883074
1
cell line: EGFP-10a+ MDA-MB-231,protocol: supplemented with 1:1 ratio of MSC
417 East 68th Street
New York
USA
Memorial Sloan-Kettering Cancer Center
Xin,,Jin
Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, the whole tumor were harvested and cut into small pieces. Tumor slices were lysed in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing libraries were constructed with 500ng polysome-associated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina).
GSM1060354
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215402,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883075
GSM1060354
GSE43306
0.08474
mammary tumor xenograft
Public on Nov 01 2013
Jan 06 2013
9606
M7
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX215402
https://www.ncbi.nlm.nih.gov/biosample/SAMN01883075
1
cell line: EGFP-10a+ MDA-MB-231,protocol: supplemented with 1:1 ratio of MSC
417 East 68th Street
New York
USA
Memorial Sloan-Kettering Cancer Center
Xin,,Jin
Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, the whole tumor were harvested and cut into small pieces. Tumor slices were lysed in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing libraries were constructed with 500ng polysome-associated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina).
GSM1060355
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215403,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883076
GSM1060355
GSE43306
0.078557
mammary tumor xenograft
Public on Nov 01 2013
Jan 06 2013
9606
M10
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX215403
https://www.ncbi.nlm.nih.gov/biosample/SAMN01883076
1
cell line: EGFP-10a+ MDA-MB-231,protocol: supplemented with 1:1 ratio of MSC
417 East 68th Street
New York
USA
Memorial Sloan-Kettering Cancer Center
Xin,,Jin
Base-calling was performed with Illumina Casava v1.8.1,Sequenced reads were mapped to hg19 of refseq from UCSC with TopHat v1.4.0,Gene-level expression counts were determined with HTSeq,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files that include gene-level expression counts
Polysome-associated RNA was extracted following the TRAP protocol from Heiman et al, Cell, 2009. Briefly, the whole tumor were harvested and cut into small pieces. Tumor slices were lysed in polysome extraction buffer. Polysomes were pulled down by anti-GFP coated sepharose beads. Polysome-associated RNA was isolated with RNAqeuous micro kit (Life Technologies).,RNA sequencing libraries were constructed with 500ng polysome-associated RNA using TruSeq RNA Sample Prep Kit v2 (Illumina).
GSM1060356
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX215404,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01883077
GSM1060356
GSE43306
0.003433
mammary tumor xenograft
Public on Nov 01 2013
Jan 06 2013
9606
M15
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX215404
https://www.ncbi.nlm.nih.gov/biosample/SAMN01883077
1
diagnosis: FLT3 positive mixed myeloid/T-cell lymphoid leukemias (MLPA),translocation: t(2;14)(q22;q32),tissue: Bone Marrow
Herestraat 49
Leuven
Belgium
KULeuven
Zeynep,,Kalender Atak
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh37.61 whole genome using TopHat v.1.3.3 with default parameters,Read counts per gene were obtained with the HTSeq package with htseq-count,The aggregated read counts were normalized with EDASeq for within-sample effects and with DESeq (Anders et al 2010 Genome Biology) for between-sample effects.,Genome_build: GRCh37.61; GRCh37.p3,Supplementary_files_format_and_content: tab-delimited text files includes normalized counts values in log2 scale
RNA extraction were performed using Trizol reagents (Invitrogen).,Illumina Truseq RNA; Next generation sequencing libraries were constructed from 500 ng of total RNA using the Truseq RNA sample prep kit (Illumina). In summary, mRNA fractions were captured on magnetic oligo(dT) beads and fragmented in to small pieces using divalent cations under elevated temperature. The mRNA fragments were reverse transcribed into first strand cDNA using random primers and reverse transcriptase (SuperScript II, Invitrogen, Carlsbad, CA, USA) and into second strand cDNA using DNA Polymerase I and RNase H. After an end-repair process and the addition of a single 'A' base, the cDNA fragments were legated to the adapter, purified and amplified by PCR to create the final cDNA libraries. Purified libraries were quality controlled on the Bioanalyzer using DNA 1000 series and quantified using the PicoGreen dsDNA quantitation assay (Invitrogen). Libraries were diluted to a 2 nM concentration and hybridized on the flow cell. Paired-end sequencing was performed on a HiSeq2000 (Illumina). Sequence reads were processed to identify gene fusion transcripts and gene expression levels.
GSM1062236
Illumina HiSeq 2000
Dec 21 2021
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX216190,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01885427
GSM1062236
GSE43417
0.01596
Bone Marrow
Public on Dec 21 2021
Jan 10 2013
9606
t(2;14)_176_10_pt.5
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX216190
https://www.ncbi.nlm.nih.gov/biosample/SAMN01885427
1
diagnosis: FLT3 positive mixed myeloid/T-cell lymphoid leukemias (MLPA),translocation: t(6;14)(q25;q32),tissue: Bone Marrow
Herestraat 49
Leuven
Belgium
KULeuven
Zeynep,,Kalender Atak
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh37.61 whole genome using TopHat v.1.3.3 with default parameters,Read counts per gene were obtained with the HTSeq package with htseq-count,The aggregated read counts were normalized with EDASeq for within-sample effects and with DESeq (Anders et al 2010 Genome Biology) for between-sample effects.,Genome_build: GRCh37.61; GRCh37.p3,Supplementary_files_format_and_content: tab-delimited text files includes normalized counts values in log2 scale
RNA extraction were performed using Trizol reagents (Invitrogen).,Illumina Truseq RNA; Next generation sequencing libraries were constructed from 500 ng of total RNA using the Truseq RNA sample prep kit (Illumina). In summary, mRNA fractions were captured on magnetic oligo(dT) beads and fragmented in to small pieces using divalent cations under elevated temperature. The mRNA fragments were reverse transcribed into first strand cDNA using random primers and reverse transcriptase (SuperScript II, Invitrogen, Carlsbad, CA, USA) and into second strand cDNA using DNA Polymerase I and RNase H. After an end-repair process and the addition of a single 'A' base, the cDNA fragments were legated to the adapter, purified and amplified by PCR to create the final cDNA libraries. Purified libraries were quality controlled on the Bioanalyzer using DNA 1000 series and quantified using the PicoGreen dsDNA quantitation assay (Invitrogen). Libraries were diluted to a 2 nM concentration and hybridized on the flow cell. Paired-end sequencing was performed on a HiSeq2000 (Illumina). Sequence reads were processed to identify gene fusion transcripts and gene expression levels.
GSM1062237
Illumina HiSeq 2000
Dec 21 2021
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX216191,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01885428
GSM1062237
GSE43417
0.097764
Bone Marrow
Public on Dec 21 2021
Jan 10 2013
9606
t(6;14)_390_11_pt.7
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX216191
https://www.ncbi.nlm.nih.gov/biosample/SAMN01885428
1
diagnosis: acute myeloid leukemia (AML),aml type: NPM1+/FLT3+,tissue: Bone Marrow
Herestraat 49
Leuven
Belgium
KULeuven
Zeynep,,Kalender Atak
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh37.61 whole genome using TopHat v.1.3.3 with default parameters,Read counts per gene were obtained with the HTSeq package with htseq-count,The aggregated read counts were normalized with EDASeq for within-sample effects and with DESeq (Anders et al 2010 Genome Biology) for between-sample effects.,Genome_build: GRCh37.61; GRCh37.p3,Supplementary_files_format_and_content: tab-delimited text files includes normalized counts values in log2 scale
RNA extraction were performed using Trizol reagents (Invitrogen).,Illumina Truseq RNA; Next generation sequencing libraries were constructed from 500 ng of total RNA using the Truseq RNA sample prep kit (Illumina). In summary, mRNA fractions were captured on magnetic oligo(dT) beads and fragmented in to small pieces using divalent cations under elevated temperature. The mRNA fragments were reverse transcribed into first strand cDNA using random primers and reverse transcriptase (SuperScript II, Invitrogen, Carlsbad, CA, USA) and into second strand cDNA using DNA Polymerase I and RNase H. After an end-repair process and the addition of a single 'A' base, the cDNA fragments were legated to the adapter, purified and amplified by PCR to create the final cDNA libraries. Purified libraries were quality controlled on the Bioanalyzer using DNA 1000 series and quantified using the PicoGreen dsDNA quantitation assay (Invitrogen). Libraries were diluted to a 2 nM concentration and hybridized on the flow cell. Paired-end sequencing was performed on a HiSeq2000 (Illumina). Sequence reads were processed to identify gene fusion transcripts and gene expression levels.
GSM1062238
Illumina HiSeq 2000
Dec 21 2021
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX216192,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01885429
GSM1062238
GSE43417
0.002116
Bone Marrow
Public on Dec 21 2021
Jan 10 2013
9606
NPM1+/FLT3+_48758
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX216192
https://www.ncbi.nlm.nih.gov/biosample/SAMN01885429
1
diagnosis: acute myeloid leukemia (AML),aml type: NPM1+/FLT3+,tissue: Bone Marrow
Herestraat 49
Leuven
Belgium
KULeuven
Zeynep,,Kalender Atak
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh37.61 whole genome using TopHat v.1.3.3 with default parameters,Read counts per gene were obtained with the HTSeq package with htseq-count,The aggregated read counts were normalized with EDASeq for within-sample effects and with DESeq (Anders et al 2010 Genome Biology) for between-sample effects.,Genome_build: GRCh37.61; GRCh37.p3,Supplementary_files_format_and_content: tab-delimited text files includes normalized counts values in log2 scale
RNA extraction were performed using Trizol reagents (Invitrogen).,Illumina Truseq RNA; Next generation sequencing libraries were constructed from 500 ng of total RNA using the Truseq RNA sample prep kit (Illumina). In summary, mRNA fractions were captured on magnetic oligo(dT) beads and fragmented in to small pieces using divalent cations under elevated temperature. The mRNA fragments were reverse transcribed into first strand cDNA using random primers and reverse transcriptase (SuperScript II, Invitrogen, Carlsbad, CA, USA) and into second strand cDNA using DNA Polymerase I and RNase H. After an end-repair process and the addition of a single 'A' base, the cDNA fragments were legated to the adapter, purified and amplified by PCR to create the final cDNA libraries. Purified libraries were quality controlled on the Bioanalyzer using DNA 1000 series and quantified using the PicoGreen dsDNA quantitation assay (Invitrogen). Libraries were diluted to a 2 nM concentration and hybridized on the flow cell. Paired-end sequencing was performed on a HiSeq2000 (Illumina). Sequence reads were processed to identify gene fusion transcripts and gene expression levels.
GSM1062239
Illumina HiSeq 2000
Dec 21 2021
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX216193,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01885430
GSM1062239
GSE43417
0.002392
Bone Marrow
Public on Dec 21 2021
Jan 10 2013
9606
NPM1+/FLT3+_48792
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX216193
https://www.ncbi.nlm.nih.gov/biosample/SAMN01885430
1
diagnosis: acute myeloid leukemia (AML),aml type: NPM1+/FLT3+,tissue: Bone Marrow
Herestraat 49
Leuven
Belgium
KULeuven
Zeynep,,Kalender Atak
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh37.61 whole genome using TopHat v.1.3.3 with default parameters,Read counts per gene were obtained with the HTSeq package with htseq-count,The aggregated read counts were normalized with EDASeq for within-sample effects and with DESeq (Anders et al 2010 Genome Biology) for between-sample effects.,Genome_build: GRCh37.61; GRCh37.p3,Supplementary_files_format_and_content: tab-delimited text files includes normalized counts values in log2 scale
RNA extraction were performed using Trizol reagents (Invitrogen).,Illumina Truseq RNA; Next generation sequencing libraries were constructed from 500 ng of total RNA using the Truseq RNA sample prep kit (Illumina). In summary, mRNA fractions were captured on magnetic oligo(dT) beads and fragmented in to small pieces using divalent cations under elevated temperature. The mRNA fragments were reverse transcribed into first strand cDNA using random primers and reverse transcriptase (SuperScript II, Invitrogen, Carlsbad, CA, USA) and into second strand cDNA using DNA Polymerase I and RNase H. After an end-repair process and the addition of a single 'A' base, the cDNA fragments were legated to the adapter, purified and amplified by PCR to create the final cDNA libraries. Purified libraries were quality controlled on the Bioanalyzer using DNA 1000 series and quantified using the PicoGreen dsDNA quantitation assay (Invitrogen). Libraries were diluted to a 2 nM concentration and hybridized on the flow cell. Paired-end sequencing was performed on a HiSeq2000 (Illumina). Sequence reads were processed to identify gene fusion transcripts and gene expression levels.
GSM1062240
Illumina HiSeq 2000
Dec 21 2021
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX216194,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01885431
GSM1062240
GSE43417
0.00183
Bone Marrow
Public on Dec 21 2021
Jan 10 2013
9606
NPM1+/FLT3+_49666
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX216194
https://www.ncbi.nlm.nih.gov/biosample/SAMN01885431
1
diagnosis: acute myeloid leukemia (AML),aml type: NPM1+/FLT3-,tissue: Bone Marrow
Herestraat 49
Leuven
Belgium
KULeuven
Zeynep,,Kalender Atak
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh37.61 whole genome using TopHat v.1.3.3 with default parameters,Read counts per gene were obtained with the HTSeq package with htseq-count,The aggregated read counts were normalized with EDASeq for within-sample effects and with DESeq (Anders et al 2010 Genome Biology) for between-sample effects.,Genome_build: GRCh37.61; GRCh37.p3,Supplementary_files_format_and_content: tab-delimited text files includes normalized counts values in log2 scale
RNA extraction were performed using Trizol reagents (Invitrogen).,Illumina Truseq RNA; Next generation sequencing libraries were constructed from 500 ng of total RNA using the Truseq RNA sample prep kit (Illumina). In summary, mRNA fractions were captured on magnetic oligo(dT) beads and fragmented in to small pieces using divalent cations under elevated temperature. The mRNA fragments were reverse transcribed into first strand cDNA using random primers and reverse transcriptase (SuperScript II, Invitrogen, Carlsbad, CA, USA) and into second strand cDNA using DNA Polymerase I and RNase H. After an end-repair process and the addition of a single 'A' base, the cDNA fragments were legated to the adapter, purified and amplified by PCR to create the final cDNA libraries. Purified libraries were quality controlled on the Bioanalyzer using DNA 1000 series and quantified using the PicoGreen dsDNA quantitation assay (Invitrogen). Libraries were diluted to a 2 nM concentration and hybridized on the flow cell. Paired-end sequencing was performed on a HiSeq2000 (Illumina). Sequence reads were processed to identify gene fusion transcripts and gene expression levels.
GSM1062244
Illumina HiSeq 2000
Dec 21 2021
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX216198,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01885435
GSM1062244
GSE43417
0.002808
Bone Marrow
Public on Dec 21 2021
Jan 10 2013
9606
NPM1+/FLT3-_49213
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX216198
https://www.ncbi.nlm.nih.gov/biosample/SAMN01885435
1
diagnosis: acute myeloid leukemia (AML),aml type: PML-RARa/FLT3+,tissue: Bone Marrow
Herestraat 49
Leuven
Belgium
KULeuven
Zeynep,,Kalender Atak
Illumina Casava1.8 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh37.61 whole genome using TopHat v.1.3.3 with default parameters,Read counts per gene were obtained with the HTSeq package with htseq-count,The aggregated read counts were normalized with EDASeq for within-sample effects and with DESeq (Anders et al 2010 Genome Biology) for between-sample effects.,Genome_build: GRCh37.61; GRCh37.p3,Supplementary_files_format_and_content: tab-delimited text files includes normalized counts values in log2 scale
RNA extraction were performed using Trizol reagents (Invitrogen).,Illumina Truseq RNA; Next generation sequencing libraries were constructed from 500 ng of total RNA using the Truseq RNA sample prep kit (Illumina). In summary, mRNA fractions were captured on magnetic oligo(dT) beads and fragmented in to small pieces using divalent cations under elevated temperature. The mRNA fragments were reverse transcribed into first strand cDNA using random primers and reverse transcriptase (SuperScript II, Invitrogen, Carlsbad, CA, USA) and into second strand cDNA using DNA Polymerase I and RNase H. After an end-repair process and the addition of a single 'A' base, the cDNA fragments were legated to the adapter, purified and amplified by PCR to create the final cDNA libraries. Purified libraries were quality controlled on the Bioanalyzer using DNA 1000 series and quantified using the PicoGreen dsDNA quantitation assay (Invitrogen). Libraries were diluted to a 2 nM concentration and hybridized on the flow cell. Paired-end sequencing was performed on a HiSeq2000 (Illumina). Sequence reads were processed to identify gene fusion transcripts and gene expression levels.
GSM1062249
Illumina HiSeq 2000
Dec 21 2021
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX216203,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01885440
GSM1062249
GSE43417
0.003591
Bone Marrow
Public on Dec 21 2021
Jan 10 2013
9606
PML-RARa/FLT3+_45095
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX216203
https://www.ncbi.nlm.nih.gov/biosample/SAMN01885440
1
cell type: Foreskin fibroblasts,extraction time: 0h after Bru labeling,treatment: Control,stranded: TRUE
NCRC, B520 Room 1346 2800 Plymouth Rd.
Ann Arbor
USA
University of Michigan
Mats,,Ljungman
Library strategy: Bru-Seq,Illumina Casava v1.8.2 software used for basecalling.,Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1,Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3,A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length,Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score; (6) strand; (7) gene length; (8) feature type – exon, intron, etc; (9) number of introns and exons; (10) feautre length; (11) hits count; (12) density – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013,Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.
GSM1062445
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
Alternative to: GSM1183334,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX216322,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01886041
GSM1062445
GSE43440
0.023534
Foreskin fibroblasts
Public on Jan 29 2013
Jan 11 2013
9606
nf0h3a
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX216322
https://www.ncbi.nlm.nih.gov/biosample/SAMN01886041
1
cell type: Foreskin fibroblasts,extraction time: 0h after Bru labeling,treatment: Control,stranded: TRUE
NCRC, B520 Room 1346 2800 Plymouth Rd.
Ann Arbor
USA
University of Michigan
Mats,,Ljungman
Library strategy: Bru-Seq,Illumina Casava v1.8.2 software used for basecalling.,Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1,Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3,A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length,Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score; (6) strand; (7) gene length; (8) feature type – exon, intron, etc; (9) number of introns and exons; (10) feautre length; (11) hits count; (12) density – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013,Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.
GSM1062446
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
Alternative to: GSM1183335,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX216323,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01886042
GSM1062446
GSE43440
0.052972
Foreskin fibroblasts
Public on Jan 29 2013
Jan 11 2013
9606
nf0h3b
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX216323
https://www.ncbi.nlm.nih.gov/biosample/SAMN01886042
1
cell type: Foreskin fibroblasts,extraction time: 0h after Bru labeling,treatment: Control,stranded: TRUE
NCRC, B520 Room 1346 2800 Plymouth Rd.
Ann Arbor
USA
University of Michigan
Mats,,Ljungman
Library strategy: Bru-Seq,Illumina Casava v1.8.2 software used for basecalling.,Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1,Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3,A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length,Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score; (6) strand; (7) gene length; (8) feature type – exon, intron, etc; (9) number of introns and exons; (10) feautre length; (11) hits count; (12) density – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013,Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.
GSM1062447
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
Reanalyzed by: GSM1954439,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX216324,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01886043
GSM1062447
GSE43440
0.055123
Foreskin fibroblasts
Public on Jan 29 2013
Jan 11 2013
9606
nf0h4
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX216324
https://www.ncbi.nlm.nih.gov/biosample/SAMN01886043
1
cell type: Foreskin fibroblasts,extraction time: 6h after Bru labeling,treatment: Control,stranded: TRUE
NCRC, B520 Room 1346 2800 Plymouth Rd.
Ann Arbor
USA
University of Michigan
Mats,,Ljungman
Library strategy: Bru-Seq,Illumina Casava v1.8.2 software used for basecalling.,Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1,Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3,A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length,Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score; (6) strand; (7) gene length; (8) feature type – exon, intron, etc; (9) number of introns and exons; (10) feautre length; (11) hits count; (12) density – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013,Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.
GSM1062449
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX216326,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01886045
GSM1062449
GSE43440
0.045068
Foreskin fibroblasts
Public on Jan 29 2013
Jan 11 2013
9606
nf6h3b
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX216326
https://www.ncbi.nlm.nih.gov/biosample/SAMN01886045
1
cell type: Foreskin fibroblasts,extraction time: 0h after Bru labeling,treatment: TNF exposure prior to Bru labeling,stranded: FALSE
NCRC, B520 Room 1346 2800 Plymouth Rd.
Ann Arbor
USA
University of Michigan
Mats,,Ljungman
Library strategy: Bru-Seq,Illumina Casava v1.8.2 software used for basecalling.,Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1,Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3,A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length,Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score; (6) strand; (7) gene length; (8) feature type – exon, intron, etc; (9) number of introns and exons; (10) feautre length; (11) hits count; (12) density – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013,Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.
GSM1062450
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX216327,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01886046
GSM1062450
GSE43440
0.033162
Foreskin fibroblasts
Public on Jan 29 2013
Jan 11 2013
9606
tnfpre0h1
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX216327
https://www.ncbi.nlm.nih.gov/biosample/SAMN01886046
1
cell type: Foreskin fibroblasts,extraction time: 0h after Bru labeling,treatment: TNF exposure prior to Bru labeling,stranded: TRUE
NCRC, B520 Room 1346 2800 Plymouth Rd.
Ann Arbor
USA
University of Michigan
Mats,,Ljungman
Library strategy: Bru-Seq,Illumina Casava v1.8.2 software used for basecalling.,Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1,Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3,A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length,Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score; (6) strand; (7) gene length; (8) feature type – exon, intron, etc; (9) number of introns and exons; (10) feautre length; (11) hits count; (12) density – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013,Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.
GSM1062451
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX216328,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01886047
GSM1062451
GSE43440
0.071973
Foreskin fibroblasts
Public on Jan 29 2013
Jan 11 2013
9606
tnfpre0h2
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX216328
https://www.ncbi.nlm.nih.gov/biosample/SAMN01886047
1
sample type: Human Fib X Human Fib Homokaryons,cell line(s): human fibroblast
269 Campus Drive
Stanford
USA
Stanford University
Jennifer,,Brady
Illumina Casava1.7 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence to 50bp and mapped to hg19 and mm10 after removal of mouse and human rRNA sequences.,Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using SeqMap. Reads mapping to both organisms were removed. To account for removal of the homologous reads, a mathematical correction was introduced to calculate the effective transcript length (exon length) in which the "effective transcript length" is equal to the "original transcript length - 50bp - 1bp for every unique 50bp sequence read which matched perfectly between mouse and human" for that particular transcript.,Genome_build: hg19 and mm10,Supplementary_files_format_and_content: .txt files include mouse and human RPKM values for each Sample. Transcripts with RPKM values of zero have been removed.
At least 30,000 heterokaryons were FACS sorted and total RNA was extracted using the Qiagen RNeasy Micro Kit. Poly A enrichment was performed with Oligo dT bead selection. The resulting poly-A+ RNA was fragmented and cDNA was synthesized using Superscript II and random primers.,Libraries were prepared according to standard Illumina protocol, using the NEB Next modules for library construction.
GSM1065157
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
polyA RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX217757,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01888202
GSM1065157
GSE43549
0.01233
Human Fib X Human Fib Homokaryons
Public on Aug 28 2013
Jan 16 2013
9606
Homokaryon Sample
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX217757
https://www.ncbi.nlm.nih.gov/biosample/SAMN01888202
1
storage method: Pelleted storage,purification method: Somatic Cell Lysis Buffer
275 E. Hancock
Detroit
USA
Wayne State University School of Medicine
Stephen,,Krawetz
Image analysis, base calling and FASTQ generation were performed using the genome analyzer pipeline software CASAVA (version 1.8.2).,Inline demultiplexing was performed using software fastq_multx (Aronesty 2011),Sequencing reads were mapped to hg19 of the human reference genome (NCBI genome build 37.2) plus human ribosomal 5S, 18S and 28S sequences using Novoalign (Novocraft Technologies v.2.08, Selangor, Malaysia) paired-end base default parameters.,The relative abundance of each transcript was calculated using Genomatix software (www.genomatix.de) and presented as FPKM (fragments per kilobase exon per million fragments mapped).,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include each read's mapping location on reference genome
Semen samples was collected in liquefied fraction, or pelleted fraction, then treated with PureSperm gradient centrifugation through a 50% PureSperm cushion, or Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100).,The RNA-Seq libraries for each sperm sample were prepared in two stages using the Nugen Ovation kit (Nugen Inc., San Carlos, CA) for cDNA synthesis and amplification plus the Nugen Encore system for library preparation. The cDNA samples were subject to single primer isothermal amplification (SPIA) prior to sequencing library preparation. In brief, 20 ng of total RNA was subject to reverse-transcription. The cDNA synthesis used oligo dT and random hexamer primers followed by isothermal amplification (SPIA). The amplified cDNA was then fragmented by covaris sonicator and the fragment ends were repaired. The Illumina compatible PE adaptors with inline barcodes were ligated onto the cDNA products followed by 15 cycles of PCR enrichment.
GSM1065928
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX218252,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01889162
GSM1065928
GSE43586
0.175629
Fertile mature sperm
Public on Dec 09 2013
Jan 17 2013
9606
S3P-SCLB
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX218252
https://www.ncbi.nlm.nih.gov/biosample/SAMN01889162
1
storage method: Liquefied storage,purification method: PureSperm cushion
275 E. Hancock
Detroit
USA
Wayne State University School of Medicine
Stephen,,Krawetz
Image analysis, base calling and FASTQ generation were performed using the genome analyzer pipeline software CASAVA (version 1.8.2).,Inline demultiplexing was performed using software fastq_multx (Aronesty 2011),Sequencing reads were mapped to hg19 of the human reference genome (NCBI genome build 37.2) plus human ribosomal 5S, 18S and 28S sequences using Novoalign (Novocraft Technologies v.2.08, Selangor, Malaysia) paired-end base default parameters.,The relative abundance of each transcript was calculated using Genomatix software (www.genomatix.de) and presented as FPKM (fragments per kilobase exon per million fragments mapped).,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include each read's mapping location on reference genome
Semen samples was collected in liquefied fraction, or pelleted fraction, then treated with PureSperm gradient centrifugation through a 50% PureSperm cushion, or Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100).,The RNA-Seq libraries for each sperm sample were prepared in two stages using the Nugen Ovation kit (Nugen Inc., San Carlos, CA) for cDNA synthesis and amplification plus the Nugen Encore system for library preparation. The cDNA samples were subject to single primer isothermal amplification (SPIA) prior to sequencing library preparation. In brief, 20 ng of total RNA was subject to reverse-transcription. The cDNA synthesis used oligo dT and random hexamer primers followed by isothermal amplification (SPIA). The amplified cDNA was then fragmented by covaris sonicator and the fragment ends were repaired. The Illumina compatible PE adaptors with inline barcodes were ligated onto the cDNA products followed by 15 cycles of PCR enrichment.
GSM1065929
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX218253,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01889163
GSM1065929
GSE43586
0.021765
Fertile mature sperm
Public on Dec 09 2013
Jan 17 2013
9606
S4L-PS
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX218253
https://www.ncbi.nlm.nih.gov/biosample/SAMN01889163
1
storage method: Liquefied storage,purification method: Somatic Cell Lysis Buffer
275 E. Hancock
Detroit
USA
Wayne State University School of Medicine
Stephen,,Krawetz
Image analysis, base calling and FASTQ generation were performed using the genome analyzer pipeline software CASAVA (version 1.8.2).,Inline demultiplexing was performed using software fastq_multx (Aronesty 2011),Sequencing reads were mapped to hg19 of the human reference genome (NCBI genome build 37.2) plus human ribosomal 5S, 18S and 28S sequences using Novoalign (Novocraft Technologies v.2.08, Selangor, Malaysia) paired-end base default parameters.,The relative abundance of each transcript was calculated using Genomatix software (www.genomatix.de) and presented as FPKM (fragments per kilobase exon per million fragments mapped).,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include each read's mapping location on reference genome
Semen samples was collected in liquefied fraction, or pelleted fraction, then treated with PureSperm gradient centrifugation through a 50% PureSperm cushion, or Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100).,The RNA-Seq libraries for each sperm sample were prepared in two stages using the Nugen Ovation kit (Nugen Inc., San Carlos, CA) for cDNA synthesis and amplification plus the Nugen Encore system for library preparation. The cDNA samples were subject to single primer isothermal amplification (SPIA) prior to sequencing library preparation. In brief, 20 ng of total RNA was subject to reverse-transcription. The cDNA synthesis used oligo dT and random hexamer primers followed by isothermal amplification (SPIA). The amplified cDNA was then fragmented by covaris sonicator and the fragment ends were repaired. The Illumina compatible PE adaptors with inline barcodes were ligated onto the cDNA products followed by 15 cycles of PCR enrichment.
GSM1065930
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX218254,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01889164
GSM1065930
GSE43586
0.150116
Fertile mature sperm
Public on Dec 09 2013
Jan 17 2013
9606
S4L-SCLB
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX218254
https://www.ncbi.nlm.nih.gov/biosample/SAMN01889164
1
storage method: Pelleted storage,purification method: PureSperm cushion
275 E. Hancock
Detroit
USA
Wayne State University School of Medicine
Stephen,,Krawetz
Image analysis, base calling and FASTQ generation were performed using the genome analyzer pipeline software CASAVA (version 1.8.2).,Inline demultiplexing was performed using software fastq_multx (Aronesty 2011),Sequencing reads were mapped to hg19 of the human reference genome (NCBI genome build 37.2) plus human ribosomal 5S, 18S and 28S sequences using Novoalign (Novocraft Technologies v.2.08, Selangor, Malaysia) paired-end base default parameters.,The relative abundance of each transcript was calculated using Genomatix software (www.genomatix.de) and presented as FPKM (fragments per kilobase exon per million fragments mapped).,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include each read's mapping location on reference genome
Semen samples was collected in liquefied fraction, or pelleted fraction, then treated with PureSperm gradient centrifugation through a 50% PureSperm cushion, or Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100).,The RNA-Seq libraries for each sperm sample were prepared in two stages using the Nugen Ovation kit (Nugen Inc., San Carlos, CA) for cDNA synthesis and amplification plus the Nugen Encore system for library preparation. The cDNA samples were subject to single primer isothermal amplification (SPIA) prior to sequencing library preparation. In brief, 20 ng of total RNA was subject to reverse-transcription. The cDNA synthesis used oligo dT and random hexamer primers followed by isothermal amplification (SPIA). The amplified cDNA was then fragmented by covaris sonicator and the fragment ends were repaired. The Illumina compatible PE adaptors with inline barcodes were ligated onto the cDNA products followed by 15 cycles of PCR enrichment.
GSM1065931
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX218255,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01889165
GSM1065931
GSE43586
0
Fertile mature sperm
Public on Dec 09 2013
Jan 17 2013
9606
S4P-PS
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX218255
https://www.ncbi.nlm.nih.gov/biosample/SAMN01889165
1
storage method: Pelleted storage,purification method: Somatic Cell Lysis Buffer
275 E. Hancock
Detroit
USA
Wayne State University School of Medicine
Stephen,,Krawetz
Image analysis, base calling and FASTQ generation were performed using the genome analyzer pipeline software CASAVA (version 1.8.2).,Inline demultiplexing was performed using software fastq_multx (Aronesty 2011),Sequencing reads were mapped to hg19 of the human reference genome (NCBI genome build 37.2) plus human ribosomal 5S, 18S and 28S sequences using Novoalign (Novocraft Technologies v.2.08, Selangor, Malaysia) paired-end base default parameters.,The relative abundance of each transcript was calculated using Genomatix software (www.genomatix.de) and presented as FPKM (fragments per kilobase exon per million fragments mapped).,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include each read's mapping location on reference genome
Semen samples was collected in liquefied fraction, or pelleted fraction, then treated with PureSperm gradient centrifugation through a 50% PureSperm cushion, or Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100).,The RNA-Seq libraries for each sperm sample were prepared in two stages using the Nugen Ovation kit (Nugen Inc., San Carlos, CA) for cDNA synthesis and amplification plus the Nugen Encore system for library preparation. The cDNA samples were subject to single primer isothermal amplification (SPIA) prior to sequencing library preparation. In brief, 20 ng of total RNA was subject to reverse-transcription. The cDNA synthesis used oligo dT and random hexamer primers followed by isothermal amplification (SPIA). The amplified cDNA was then fragmented by covaris sonicator and the fragment ends were repaired. The Illumina compatible PE adaptors with inline barcodes were ligated onto the cDNA products followed by 15 cycles of PCR enrichment.
GSM1065932
Illumina HiSeq 2000
May 15 2019
cDNA
transcriptomic
RNA-Seq
total RNA
Homo sapiens
GPL11154
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX218256,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01889166
GSM1065932
GSE43586
0.041607
Fertile mature sperm
Public on Dec 09 2013
Jan 17 2013
9606
S4P-SCLB
SRA
https://www.ncbi.nlm.nih.gov/sra?term=SRX218256
https://www.ncbi.nlm.nih.gov/biosample/SAMN01889166