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Sample GSM2635752 Query DataSets for GSM2635752
Status Public on Nov 15, 2017
Title BG4-ChIP-rep1
Sample type SRA
 
Source name HaCaT cell line
Organism Homo sapiens
Characteristics cell line: HaCaT
Treatment protocol NA
Growth protocol HaCaT cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% FBS.
Extracted molecule genomic DNA
Extraction protocol Chromatin was isolated from HaCaT 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. For further details see methods section in the associated manuscript.
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 following paper https://doi.org/10.1038/ng.3662. 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/.
 
Submission date May 23, 2017
Last update date May 15, 2019
Contact name Giovanni Marsico
E-mail(s) persego@gmail.com
Organization name CRUK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platform ID GPL18573
Series (1)
GSE99205 Chromatin immunoprecipitation for genome-wide mapping of endogenous G-quadruplex DNA structures
Relations
BioSample SAMN07157024
SRA SRX2844869

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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