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Sample GSM1579373 Query DataSets for GSM1579373
Status Public on May 04, 2015
Title GROseq Activin (+ chain)
Sample type SRA
Source name H1 human ESCs
Organism Homo sapiens
Characteristics cell type: embryonic stem cells
passages/media: 40-50/mTeSR
treatment: Activin A 6h
Treatment protocol H1 hESCs were left untreated, or treated with Wnt3a (200ng/ml), Activin (100ng/ml), or both cytokines together for 4h (ChIPseq) or 6h (GRO-seq). For siRNA-GROseq experiments, hESCs were transfected with specific siRNAs (using RNAimax) 48h before adding cytokine treatments.
Growth protocol H1 hESCs grown in mTeSR media
Extracted molecule total RNA
Extraction protocol For ChIPseq, DNA was extracted Qiaquick PCR extraction kit (cat 28106, Qiagen). For GROseq, nascent RNA purification was done using Trizol LS (Invitrogene).
For ChIPseq, libraries were done with Illumina reagents. For GROseq, libraries were prepared with NEBnext kit (E7300S)
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2500
Description Nascent RNA
Data processing Peak calling was performed using Homer software
Genome_build: hg19
Supplementary_files_format_and_content: wig
Submission date Jan 07, 2015
Last update date May 15, 2019
Contact name conchi estaras
Organization name The Salk Institute
Department Regulatory Biology
Lab Jones lab
Street address 10010 N Torrey Pines Rd
City La Jolla, San Diego
State/province CA
ZIP/Postal code 92037
Country USA
Platform ID GPL16791
Series (1)
GSE64758 Wnt3a-Activin A Synergy Induces eRNAPII Pause-Release and Counteracts a Yap1 Elongation Block during hESC Differentiation
BioSample SAMN03278036
SRA SRX833430
Named Annotation GSM1579373_Activin_1.ucsc.bigWig

Supplementary file Size Download File type/resource
GSM1579373_Activin_1.ucsc.bigWig 87.8 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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