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Sample GSM2040043 Query DataSets for GSM2040043
Status Public on Oct 24, 2016
Title MCF7_ChIP_ERa_sc543x_NA_E2_100nM_120min_Rep1
Sample type SRA
 
Source name MCF7-E2-CHIP-ERA
Organism Homo sapiens
Characteristics cell line: MCF7 (ATCC, HTB-22)
cell type: Breast adenocarcinoma-derived cells
passages: N/A
treated with: 100nM E2, 120min
chip antibody: Era (Santa-Cruz, sc543x, lot:
Treatment protocol For EtOH treatment, 250 ul of 1% EtOH were added directly to cell medium (25 ml) and incubated for 1 hour at 37C. For estradiol treatment, 100nM of Beta-Estradiol (SIGMA, E8875) was added directly to cell medium and incubated for two hours at 37C.
Growth protocol HEPG2 were grown in DMEM (Gibco, 11965-092) and A549 were grown in F12K medium (Gibco, 21127022) as recommended by the supplier. All cell mediums were supplemented with 10% fetal bovine serum (Invitrogen, qualified 12483020), 100 μM MEM nonessential amino acids (Cellgro, 25-0250), 2 mM L-glutamine (Gibco, 25030-081), 100 U/ml penicillin, 100 μg/ml streptomycin (Gibco, 15170-063). MCF7 were kept in DMEM w/o phenol-red (Gibco, 31053-028) supplemented with 5% of Charcoal/Dextran treated FBS (Hyclone, AVH78911), 100 μM MEM nonessential amino acids (Cellgro, 25-0250) and 2 mM L-glutamine (Gibco, 25030-081) for 3 days prior to 100nM of Beta-Estradiol (SIGMA, E8875) for two hours.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked with 1% formaldehyde in culture medium for 10 minutes at room temperature. Cells were then lysed in 10 ml lysis buffer (0.1%SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl ph 8.0 and 150 mM NaCl) and chromatin was sheared to 200-600 bp fragments using a Bioruptor Sonicator (Diagenode). Chromatin extract from 5x10^7 cells was incubated overnight at 4oC with 100 ul of Dynabeads Protein G magnetic beads (Life Technologies, 10004D) previously incubated with 10 ug of selected antibodies. After ChIP, samples were washed and bound complex were reversed cross-linked and eluted in 10mM Tris-HCl pH 8
The TruSeq DNA sample prep kit with indexing adapters was used according to the manufacturer's recommendations (Illumina)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description MCF7-E2-CHIP-ERA-rep1
Data processing All datasets were analyzed with the ChIP-Seq pipeline developed at the McGill University and Génome Québec Innovation Centre (https://bitbucket.org/mugqic/mugqic_pipelinest) (version 2.1.0)
All samples were processed using Trimmomatic 0.33 with the following parameters: LEADING=30, TRAILING=30, SLIDINGWINDOW=4:30, MINLEN=30. Reads were mapped against the hg19 build of the human reference genome using BWA 0.7.12 with default parameters and MACS2 2.1.0 with default parameters was used for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak files were generated with MACS2 2.1.0 with default parameters. The enrichment ratio of each replicate were calculated with the 2 control files available for each cell line.
 
Submission date Jan 14, 2016
Last update date May 15, 2019
Contact name Steve Bilodeau
E-mail(s) Steve.Bilodeau@crchudequebec.ulaval.ca
Phone 418 525-4444 15550
Organization name Centre de recherche du CHU de Québec
Street address 9 McMahon
City Quebec
State/province Quebec
ZIP/Postal code G1R 2J6
Country Canada
 
Platform ID GPL11154
Series (1)
GSE76893 FOXA and master transcription factors recruit Mediator and Cohesin to the core transcriptional regulatory circuitry of cancer cells
Relations
BioSample SAMN04415520
SRA SRX1531791

Supplementary file Size Download File type/resource
GSM2040043_MCF7_GB_E2_Era_2WCE_rep1_peaks.narrowPeak.gz 1.7 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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