|
| Status |
Public on Feb 01, 2010 |
| Title |
MCF7_E2_ER |
| Sample type |
SRA |
| |
|
| Source name |
MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: estrogen-responsive breast cancer
antibody: Estrogen Receptor (ER)
treatment variable: hormone starved for 3 days, treated with 10 nM β-estradiol for 45 minutes
|
| Treatment protocol |
Hormone-starved cells were treated with 1% ethanol (ethl) or 10nM beta-estraidiol for 45 min.
|
| Growth protocol |
MCF7 cells were grown to 50% confluence in RPMI + 10% FBS, changed to the starving medium (RPMI with 5% FCS) for 3 days, prior to treatment by ethanol (ethl) or 10nM beta-estradiol (E2).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). 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 15 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 |
| |
|
| Description |
Chromatin IP against ER
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the human (hg18; March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 250 bp to create summary windows.
Peaks: Peak detection was performed with the Hpeak algorithm (http://www.sph.umich.edu/csg/qin/HPeak/). The single Peak file 'MCF7_E2-ethl.hpeak.out' comparing E2 and ethl-treated (control) samples is attached to the Series record.
Please see readme files attached to the Series record for additional information about data files.
|
| |
|
| Submission date |
Nov 13, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Jindan Yu |
| E-mail(s) |
jindan-yu@northwestern.edu
|
| Organization name |
Northwestern University
|
| Department |
Medicine - Hem/Onc
|
| Lab |
Yu
|
| Street address |
303 E. Superior St.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE19013 |
ChIP-Seq analysis of ER binding sites in MCF7 breast cancer cells |
|
| Relations |
| SRA |
SRX016327 |
| BioSample |
SAMN00008418 |
