|
| Status |
Public on Sep 19, 2009 |
| Title |
GATA1_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Chromatin IP against GATA1
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: GATA1
cell line: G1E ER4
|
| Treatment protocol |
G1E-ER4 cells growing in log phase were induced for 24 hours with 20nM estradiol.
|
| Growth protocol |
G1E-ER4 cells were cultured as described previously. Weiss MJ, Yu C, Orkin SH. Erythroid-cell-specific properties of transcription factor GATA-1 revealed by phenotypic rescue of a gene-targeted cell line. Mol Cell Biol. 1997;17: 1642-1651.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and GATA1-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the ChIP Sequencing of DNA Kit (Part# 11257047). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Induced G1E ER4 cells
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the mouse (Feb. 2006 mm8) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
|
| |
|
| Submission date |
Sep 18, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Ross Hardison |
| E-mail(s) |
rch8@psu.edu
|
| Organization name |
Pennsylvania State University
|
| Street address |
303 Wartik Lab
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE18164 |
Genome-wide maps of GATA1 occupany in induced G1E ER4 cell line. |
|
| Relations |
| Reanalyzed by |
GSM897224 |
| SRA |
SRX013185 |
| BioSample |
SAMN00005327 |
