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Sample GSM3149035 Query DataSets for GSM3149035
Status Public on Dec 27, 2018
Title MCF7_H3K4me3_DSG
Sample type SRA
 
Source name MCF7 cell line
Organism Homo sapiens
Characteristics chip antibody: H3K4me3 (Abcam; ab8580)
patient id: MCF7_H3K4me3_DSG
case/control: DSG
Treatment protocol Surgical resections from Prostate, breast and endometrium tumors.
Growth protocol fresh frozen material
Extracted molecule genomic DNA
Extraction protocol Chromatin immunoprecipitations were performed as described previously with minor changes (Zwart et al., 2013). Samples were crosslinked in solution A with 2mM DSG (CovaChem) for 25 minutes at room temperature. After 25 minutes, 1% formaldehyde was added for 20 minutes and subsequently quenched with glycine. Samples were lysed as described (Schmidt et al., 2009) and sonicated for at least 10 cycles of 30s on, 30s off using a Diagenode Bioruptor Pico. For each ChIP, 5ug of antibody was conjugated with 50ul Protein A magnetic beads. Antibodies used were AR (sc-816, Santa Cruz), H3K27ac (39133, Active Motif), H3K4me3 (Ab8580, Abcam) and H3K27me3 (39155, Active Motif). Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing Sequences were generated by the Illumina Hiseq 2500 genome analyser (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (Ensembl release 55: Homosapiens GRCh 37.55) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.
Genome_build: GRCh 37.55
 
Submission date May 21, 2018
Last update date Dec 27, 2018
Contact name Abhishek Singh
E-mail(s) abhisheksinghnl@gmail.com
Organization name Netherlands Cancer Institute
Street address Plesmanlaan
City Amsterdam
ZIP/Postal code 1066CX
Country Netherlands
 
Platform ID GPL16791
Series (1)
GSE114737 Optimized ChIP-seq procedure facilitates hormone receptor profiling in human tumors
Relations
BioSample SAMN09238289
SRA SRX4115997

Supplementary file Size Download File type/resource
GSM3149035_MCF7_H3K4me3_DSG.bed.gz 148.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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