|
| Status |
Public on Mar 09, 2009 |
| Title |
ERalpha Tam |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
Tamoxifen treated 1 uM 1h
Antibody ERalpha
|
| Treatment protocol |
MCF-7 cells were treated for 1h with the different compounds
|
| Growth protocol |
MCF-7 cells were hormone starved for 48h in DMEM w/o phenolred supplemented with 5% charcoal treated serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was harvested after 1h induction. Chromatin was fixed in 1% formaldehyde for 30 minutes, sonicated for 15x30sec at high power using a Bioruptor (Diagenode), immunoprecipitated ERalpha (AC-066-100, Diagenode) and RNAPII ((AC-0555-100, Diagenode) antibodies, purified and sequenced using Illumina Genome Analyzer as recommended by the manufacturer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against ERalpha
|
| Data processing |
Reads (32 bp) were aligned to the human (Homo sapiens, hg18) reference genome and extended to 133 bp. RNAPII tracks for the different ligands were equalized for the total number of mapped tags by random removal of sequenced tags. For ERalpha enriched regions were identified using Findpeaks. For RNAPII the number of tags within each ENSEMBL gene body was counted and gene regulation of each gene was expressed as the ratio of tags of ligand induced versus control.
|
| |
|
| Submission date |
Jan 30, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
H.G. Stunnenberg |
| E-mail(s) |
h.stunnenberg@ncmls.ru.nl
|
| Phone |
+31-24-3610520
|
| Organization name |
Radboud University
|
| Department |
Department of Molecular Biology (274)
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE14664 |
ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands |
|
| Relations |
| SRA |
SRX003939 |
| BioSample |
SAMN02195448 |
