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Sample GSM2345029 Query DataSets for GSM2345029
Status Public on Jul 13, 2017
Title K562_BRD4_rep1
Sample type SRA
 
Source name K562_BRD4
Organism Homo sapiens
Characteristics cell line: K562
tissue source: bone marrow
cell line: K562
chip antibody: anti-BRD4 (E2A7X, Cell Signalling)
Growth protocol MV4;11 cells were grown in RPMI-1640 supplemented with 20% FBS, penicillin (100 U/mL), streptomycin (100 µg/mL). K562 cells were grown in MEM medium supplemented with 1% pyruvate, 1% NAA and 10% FBS.
Extracted molecule genomic DNA
Extraction protocol Lysate were isolated from formaldehybe cross-linked cells and digested with micrococcal nuclease to mononucleosomes, then immunoprecipitated with antibody
NEBNext ChIP-seq library prep master mix set
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the human genome (G1k V37) using bwa 0.6.2-r126
Peak-calling was performed using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bed files from MACS2 for each sample
 
Submission date Oct 14, 2016
Last update date May 15, 2019
Contact name Mark Dawson
E-mail(s) mark.dawson@petermac.org
Organization name Peter MacCallum Cancer Centre
Street address 305 Grattan Street
City Melbourne
State/province VIC
ZIP/Postal code 3000
Country Australia
 
Platform ID GPL11154
Series (2)
GSE88747 Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies [ChIP-seq 2]
GSE88751 Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies
Relations
BioSample SAMN05908479
SRA SRX2245491

Supplementary file Size Download File type/resource
GSM2345029_K562_BRD4_1_peaks.bed.gz 297.7 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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