|
| Status |
Public on Sep 25, 2014 |
| Title |
HSPC DMSO FAIRE Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
CD34+ HSPCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD34+ HSPCs
treatment: DMSO Control
|
| Treatment protocol |
Cells were treated with 2uM UNC0638 for 48 hours, as described previously (Chen et al., 2012 Genes Dev 26:2499-2511)
|
| Growth protocol |
CD34+ cells were obtained as described previously (Chen et al., 2012 Genes Dev 26:2499-2511). Cells were maintained in either serum-containing or serum-free media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepard according to Illumina instructions for DNA samples
|
| |
|
| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
FAIRE library DMSO replicate 1
|
| Data processing |
FAIRE-seq: FAIRE was performed as previously described (Giresi et al., 2007). Isolated DNAs were barcoded and sequenced on the Illumina HiSeq 2500 to produced 100bp x 100bp paired-end reads. Reads were aligned to the human genome (version hg19, from the UCSC Genome Browser) using Bowtie2 with local alignment.
Peak calling was performed with F-seq using default parameters and a 200bp feature length. Irreproducible Discovery Rate (IDR) analysis was performed to identify reproducible peaks.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak format, as described here: http://genome.ucsc.edu/FAQ/FAQformat.html#format12
|
| |
|
| Submission date |
Jul 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Dustin E Schones |
| E-mail(s) |
dschones@coh.org
|
| Organization name |
City of Hope
|
| Street address |
1500 E Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE59749 |
G9a/GLP-dependent H3K9me2 patterning alters chromatin structure at CpG islands in hematopoietic progenitors. |
|
| Relations |
| BioSample |
SAMN02937543 |
| SRA |
SRX661183 |
