|
| Status |
Public on Jan 01, 2015 |
| Title |
SUZ12 |
| Sample type |
SRA |
| |
|
| Source name |
Human primary fetal liver proerythroblasts (ProEs), SUZ12 ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: fetal liver
cell type: CD34+ HSPC-derived proerythroblasts
chip antibody: SUZ12 (Abcam ab12073; Active Motif 39357, lot 29111002)
|
| Treatment protocol |
NA
|
| Growth protocol |
Primary maturing fetal liver erythroblasts were generated ex vivo using a serum-free two-phase liquid culture system.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq analysis using the Illumina HiSeq 2000, 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 2000 |
| |
|
| Description |
ChIP DNA
|
| 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 window was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by HiSeq 2000.
Genome_build: NCBI36 (hg18)
Supplementary_files_format_and_content: Mapped read bed file, wig file, and peak bed file.
|
| |
|
| Submission date |
Jul 03, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Xu |
| E-mail(s) |
Jian.Xu@stjude.org
|
| Phone |
9015955208
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Pathology
|
| Street address |
262 Danny Thomas Place, MS 345
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE59087 |
ChIP-seq analysis of PRC2 core subunits in primary human erythroid progenitor cells |
| GSE59090 |
ChIP-seq and RNA-seq analysis of PRC2 core subunits in primary human erythroid progenitor cells |
|
| Relations |
| BioSample |
SAMN02902826 |
| SRA |
SRX646126 |
| Named Annotation |
GSM1427067_SUZ12-F.bed.gz |
| Named Annotation |
GSM1427067_SUZ12-F.wig.gz |
| Named Annotation |
GSM1427067_SUZ12-F_peaks.bed.gz |
