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Sample GSM1316331 Query DataSets for GSM1316331
Status Public on Mar 31, 2015
Title ES_D10_H3K4me1_rep2
Sample type SRA
 
Source name Pancreatic endoderm
Organism Homo sapiens
Characteristics cell line: CyT49
cell types: hESC derived pancreatic endoderm
antibody: H3K4me1, Abcam ab8895
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 ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing 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 SAMN02598612
SRA SRX451071

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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