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Sample GSM2876090 Query DataSets for GSM2876090
Status Public on Jul 16, 2018
Title K562_BG4-ChIP-rep_1a
Sample type SRA
Source name K562 cell line
Organism Homo sapiens
Characteristics cell line: K562
antibody: G4
Treatment protocol NA
Growth protocol K562 cells were cultured in RPMI-1640 medium supplemented with 10%FBS.
Extracted molecule genomic DNA
Extraction protocol Chromatin was isolated from K562 cells that were cross-linked using 1% formaldehyde for 10 min at RT and prepared using a ChIP-qPCR Kit (Chromatrap, cat. no. 500117). Chromatin was sonicated using a Bioruptor Plus (Diagenode) to give a fragment distribution of 100-500 bp.
G4 ChIPed DNA was subjected to Nextera library preparation (Illumina, cat. no. FC-121-1030). For further details see methods section in the associated manuscript.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing The data was processed as described in the associated manuscript. Details about the analysis can also be found at
Genome_build: hg19
Supplementary_files_format_and_content: For narrowPeak format see MACS2 documentation at A tiled data file (TDF) file (.tdf) is a binary file that contains data that has been preprocessed by igvtools for faster display in IGV.
Submission date Dec 05, 2017
Last update date Feb 11, 2020
Contact name Avazeh T Ghanbarian
Organization name University of Cambridge
Department Cancer Research UK, Cambridge Inst
Lab Balasubramanian
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
Platform ID GPL18573
Series (1)
GSE107690 G-quadruplex structures moulds the DNA methylome
Reanalyzed by GSE145090
BioSample SAMN08131883
SRA SRX3444806

Supplementary file Size Download File type/resource
GSM2876090_B_REP1.SLX-12318_9.K562_asynch_a_701_504.tdf 177.1 Mb (ftp)(http) TDF
GSM2876090_B_REP1.SLX-12318_9.K562_asynch_a_701_504_peaks.narrowPeak.gz 280.7 Kb (ftp)(http) NARROWPEAK 144.0 Mb (ftp)(http) BW
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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