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Sample GSM365927 Query DataSets for GSM365927
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

Supplementary file Size Download File type/resource
GSM365927.peaks.txt.gz 150.9 Kb (ftp)(http) TXT
GSM365927_ER_Tam_align.bed.gz 44.8 Mb (ftp)(http) BED
GSM365927_ER_Tam_peaks.bed.gz 74.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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