|
| Status |
Public on Jan 11, 2016 |
| Title |
H3K27ac-F0 |
| Sample type |
SRA |
| |
|
| Source name |
Fetal hematopoietic stem/progenitor cells (HSPCs)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Fetal HSPCs (F0)
developmental stage/tissue: fetal liver
cell type: primary fetal liver CD34+ HSPCs (F0)
chip antibody: H3K27ac
chip antibody vendor: Abcam
chip antibody cat. #: ab4729
|
| Treatment protocol |
NA
|
| Growth protocol |
Human primary fetal liver or adult bone marrow-derived CD34+ HSPCs and ProEs were cultured ex vivo using a serum-free two-phase liquid culture system.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq analysis using the Illumina HiSeq2500, 10-20 ng of ChIP DNA was processed for library generation using the ChIP-seq Sample Preparation Kit (Illumina) following the manufacturer’s protocol. Raw ChIP-seq data were processed using the Illumina software pipeline. Only ChIP-seq reads that aligned to exactly one location in the reference human genome (UCSC, hg18) were retained for downstream data analysis.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing reads were aligned to human genome assembly hg18 (NCBI version 36) using Bowtie v0.12.7 with the following parameters: -v 2 -m 3 --strata --best. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by HiSeq 2000.
Genome_build: hg18
Supplementary_files_format_and_content: Mapped read bed file, wig file, and peak bed file
|
| |
|
| Submission date |
Jul 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Xu |
| E-mail(s) |
Jian.Xu@UTSouthwestern.edu
|
| Phone |
214-648-6125
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Children's Research Institute
|
| Street address |
6000 Harry Hines Blvd. NL12.138B
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75235 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE70660 |
Dynamic control of enhancer repertoires drives lineage and developmental stage-specific transcription during human erythropoiesis |
|
| Relations |
| BioSample |
SAMN03852520 |
| SRA |
SRX1089816 |
