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Sample GSM1122654 Query DataSets for GSM1122654
Status Public on Jun 17, 2014
Title MCF7_H3K4me2ChIP_Control
Sample type SRA
 
Source name breast cancer cells
Organism Homo sapiens
Characteristics cell line: MCF7
cell type: breast cancer cells
chip antibody: H3K4me2 (Millipore, 07-030)
transfection: siControl
Treatment protocol Cells transfected with gene-specific or non-targeting siRNA pools were cultured for 5 days prior to the sample preparation.
Extracted molecule genomic DNA
Extraction protocol To isolate chromatin, formaldehyde-cross-linked nuclei were sonicated using a Covaris focused-ultrasonicator. Following ChIP performed with specific antibodies and Dynabeads® Protein G (Invitrogen)
ChIP DNA was subjected to end repair, A-tailing, ligation of Illumia single end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Basecalls performed using CASAVA version 1.7 or 1.8.
ChIP-seq raw data was mapped by Bowtie using default parameters to hg19.
Each library after mapping was randomly sampled down without replacement to 15 million reads. Only one tag from each unique position was considered to avoid PCR biases from the sequencing.
The identification of ChIP-seq enriched regions including summits was performed using version 2.0 of MACS. Regions of enrichment comparing to input control exceeding a given threshold (q < 0.001) were called as peaks.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files of called peaks were generated using MACS2
 
Submission date Apr 15, 2013
Last update date May 15, 2019
Contact name Kornelia Polyak
E-mail(s) kornelia_polyak@dfci.harvard.edu
Phone 617-632-2106
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Lab Polyak
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL11154
Series (2)
GSE46055 Genome-wide location analysis in breast cancer cell-lines
GSE46073 Gene expression and genome-wide location analysis of breast cancer cell-lines
Relations
BioSample SAMN02045871
SRA SRX265415

Supplementary file Size Download File type/resource
GSM1122654_H3K4me2-MCF7-hg19-sd-q_c3.0_l140_g50_peaks.encodePeak.peak.bed.gz 729.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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