NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1316327 Query DataSets for GSM1316327
Status Public on Mar 31, 2015
Title ES_D7_GRO_seq
Sample type SRA
 
Source name Posterior foregut
Organism Homo sapiens
Characteristics cell line: CyT49
cell types: hESC derived posterior foregut
antibody: N/A
Treatment protocol Pancreatic differentiation was performed as previously described (D'Amour et al., 2006; Kroon et al., 2008; Schulz et al., 2012). Hepatic endoderm was derived by treating the definitive endoderm stage (Day 2),with 50ng/ml BMP4 (Millipore) and 10ng/ml FGF2 (Millipore) in RPMI media (Mediatech) supplemented with 0.2% (vol/vol) FBS (HyClone) with daily feeding for six days. Suspension culture was used.
Growth protocol hESC media was comprised of DMEM/F12 (Mediatech or Life Technologies) supplemented with 10% (vol/vol) KnockOut™ Serum Replacement XenoFree (Life Technologies), 0.1 mM MEM non-essential amino acids (Life Technologies), 1X GlutaMAX™ I (Life Technologies), 1% (vol/vol) penicillin/streptomycin (Life Technologies), 0.1mM 2-mercaptoethanol (Life Technologies), 10 ng/ml Activin A (R&D Systems), and 10 ng/ml Heregulin-β1 (PeproTech).
Extracted molecule genomic DNA
Extraction protocol ChIP-seq protocol can be found from http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf. GRO-seq experiments were performed according to previous publication (Wang, D. et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390-4 (2011).). 
Libraries were prepared according to Illumina's instruction or cited literatures.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing Library strategy: GRO-Seq
fastq: Illumina's HiSeq Control Software
Each fastq file was mapped to human genome (hg18) with Bowtie. We allow up to 2 mismatches. The mapping results for two biological replicates were merged for downstream analysis. To generate the wig file, we first extended each read to 300 bp along 5' end. We then cut the genome into 100 bp bins and count how many reads fall into each bin. Finally, the wig files were converted to bigwig by using the wigToBigwig software
Genome_build: hg18
Supplementary_files_format_and_content: Experiments with two biological replicates were merged first. To generate the wig file, we extend each read to 300 bp. In cases of merged replicates, the wig data is linked to the first replicate (rep1).
 
Submission date Jan 28, 2014
Last update date May 15, 2019
Contact name Bing Ren
Organization name University of California, San Diego School of Medicine
Street address 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL16791
Series (1)
GSE54471 Developmental Competence Encoded at the Level of Enhancers
Relations
BioSample SAMN02598617
SRA SRX451067

Supplementary file Size Download File type/resource
GSM1316327_groseq.D7.fwd.bw 94.8 Mb (ftp)(http) BW
GSM1316327_groseq.D7.rev.bw 87.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap