NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2876091 Query DataSets for GSM2876091
Status Public on Jul 16, 2018
Title K562_BG4-ChIP-rep_1c
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 https://github.com/sblab-bioinformatics/dna-secondary-struct-chrom-lands/blob/master/Methods.md
Genome_build: hg19
Supplementary_files_format_and_content: For narrowPeak format see MACS2 documentation at https://github.com/taoliu/MACS/. 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 May 15, 2019
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
Relations
BioSample SAMN08131882
SRA SRX3444807

Supplementary file Size Download File type/resource
GSM2876091_B_REP1.SLX-12318_9.K562_asynch_c_703_504.tdf 172.8 Mb (ftp)(http) TDF
GSM2876091_B_REP1.SLX-12318_9.K562_asynch_c_703_504_peaks.narrowPeak.gz 225.3 Kb (ftp)(http) NARROWPEAK
GSM2876091_B_REP1.SLX-12319.K562_asynch_c_703_504.clean.bw 138.2 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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap