 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 31, 2015 |
| Title |
ES_D0_H3K4me1_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
hESC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CyT49
cell types: Undifferentiated hESCs
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 |
SAMN02598635 |
| SRA |
SRX451043 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
