Datasets:

gabrielaltay

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archs4-human-gene-v2.5-meta-sample

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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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

cells in culture