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Sample GSM1155148 Query DataSets for GSM1155148
Status Public on Jun 07, 2013
Title T47D-overexpressing ELF5-input DNA-48hour
Sample type SRA
 
Source name T47D cell line
Organism Homo sapiens
Characteristics cell line: T47D
treatment: doxycycline
timepoint: 48h
enrichment: input DNA
Treatment protocol Drug treatments were performed with Dox (Clontech) at 0.1 μg/ml, R5020 (Du Pont) at 10 nM or 17β-estradiol (Sigma) at 10 mM. Dox-containing medium was changed every 24 hours to ensure optimum Dox activity. Adherent cells on tissue culture plates were incubated in fresh, warm, serum-free medium supplemented with 1% formaldehyde, at 37°C for 10 minutes.
Growth protocol Human breast carcinoma T47D-EcoR (Musgrove et al., 2001) cell lines were grown in RPMI 1640 medium (Invitrogen) supplemented with 10 % Tet System Approved fetal bovine serum (FBS) (Clontech). Cells infected with pHUSH-ProEX-based produced by the Platinum E cell line (Morita et al., 2000). Transient transfection with plasmid constructs used FuGENE reagent (Roche) or Lipofectamine LTX (Invitrogen) according to manufacturer’s instructions. Cells were maintained in the presence of puromycin (Sigma) at a concentration of 2μg/mL.
Extracted molecule genomic DNA
Extraction protocol Cells were washed 2 times with cold PBS and scraped into 600 μl PBS with protease inhibitors (P8340, Sigma). Fixed cells were spun for 2 minutes at 6,000xg, washed as before and snap frozen in liquid nitrogen.
ChIP-Seq as previously described (doi:10.1016/j.ymeth.2009.03.001) using a 50%–50% mixture of V5-specific antibody and the Santa Cruz N20 anti ELF5 antibody, or no antibody for the input files. DNA was processed for Illumina sequencing using 36-bp reads on a GAIIx.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
 
Description T47D cell lines, overexpressing ELF5 with V5 tag, input DNA, replicate 2
Data processing Sequences were aligned against NCBI Build 36.3 of the human genome using MAQ (http://maq.sourceforge.net/) with default parameters.
The aligned reads were converted to BED format using a custom script.
Reads were filtered for uniquely mapped tags
Wiggle coverage files generated, normalised per million reads.
Genome_build: ncbi36.3
Supplementary_files_format_and_content: *.filter.bed.gz files contain the aligned reads, filtered for unique mappers only. These are standard BED6 formatted files (chr,start,stop,name=read_id,score=mapping_quality,strand)
Supplementary_files_format_and_content: *wig.gz files are standard wiggle files, at 20bp resolution, indicating read depth across the genome, normalised per 1e06 reads.
 
Submission date Jun 06, 2013
Last update date May 15, 2019
Contact name Mark Cowley
E-mail(s) m.cowley@garvan.org.au
Organization name Garvan Institute of Medical Research
Department Genome Informatics & Clinical Genomics
Lab Dinger lab
Street address 384 Victoria St.
City Darlinghurst
State/province NSW
ZIP/Postal code 2010
Country Australia
 
Platform ID GPL10999
Series (2)
GSE30407 The ets transcription factor ELF5 suppresses the estrogen sensitive phenotype and contributes to antiestrogen resistance in luminal breast cancer.
GSE31216 The ets transcription factor ELF5 suppresses the estrogen sensitive phenotype and contributes to antiestrogen resistance in luminal breast cancer. [human ChIP-Seq]
Relations
BioSample SAMN02191889
SRA SRX297111

Supplementary file Size Download File type/resource
GSM1155148_T47D_Input_CRI02.filter.bed.gz 137.0 Mb (ftp)(http) BED
GSM1155148_T47D_Input_CRI02.wig.gz 199.7 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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