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Sample GSM1969222 Query DataSets for GSM1969222
Status Public on Feb 01, 2016
Title Merged_Control_ERRa_ChIP-seq
Sample type SRA
 
Source name BT474 human breast cancer cell line treated with vehicle for 90 minutes
Organism Homo sapiens
Characteristics cell line: BT474
tissue type: Breast tumor
chip antibody: ERRa
Treatment protocol Reagents were simply added to the media for cell treatment in regular 6cm culture dish.
Growth protocol Cells were cultured in regular DMEM. 24h after seeding, media was changed and fresh media with vehicle or AICAR 0.5mM
Extracted molecule genomic DNA
Extraction protocol After 90min treatment with vehicle or AICAR, nuclei were isolated and subjected to chromatin immunoprecipitation. Following ERRa ChIP, genomic DNA was purified with QIAGEN DNA extraction kit.
Libraries were performed at the Génome Québec Innovation Centre (McGill University) using standard protocol for HiSeq - Illumina Single reads 50bp sequencing lane
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description genomic DNA enriched following ERRa chromatin immunoprecipitation
Data processing Sequences were aligned to the human genome database (Hg19) using BWA v0.5.9 (Li and Durbin, 2009)
Significant DNA binding (peak) was determined using MACS v1.4.1 software (Zhang et al., 2008).
Peak annotation, tag directory, bed file generation, and de novo motif discovery were performed with the Homer package v3.18.
Genome_build: hg19
Supplementary_files_format_and_content: data are presented as bigwig and annotated peak lists in excel from the merged of two samples for control condition and two samples for AICAR-treated cells. Additionnally, we included fastq data for each sample. All samples were run twice so there is 2 fastq files per sample (except ERRa_ChIP_AICAR_replicate 1 that has 3 fastq files).
 
Submission date Dec 10, 2015
Last update date May 15, 2019
Contact name Etienne Audet-Walsh
E-mail(s) etienne.audet-walsh@crchudequebec.ulaval.ca
Organization name Université Laval
Department Molecular Medicine
Street address 2705 boulevard Laurier
City Québec City
State/province QC
ZIP/Postal code G1V 4G2
Country Canada
 
Platform ID GPL11154
Series (2)
GSE75876 The PGC-1α/ERRα Axis Represses One-Carbon Metabolism and Promotes Sensitivity to Anti-Folate Therapy in Breast Cancer [ChIP-Seq]
GSE75877 The PGC-1α/ERRα Axis Represses One-Carbon Metabolism and Promotes Sensitivity to Anti-Folate Therapy in Breast Cancer
Relations
BioSample SAMN04329917
SRA SRX1473609

Supplementary file Size Download File type/resource
GSM1969222_Merged_Control_ERRa_ChIP-seq.bam.bigwig 3.5 Gb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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