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Sample GSM4261890 Query DataSets for GSM4261890
Status Public on Apr 29, 2021
Title WT_Input DNA_Replicate 2
Sample type SRA
 
Source name HAP1 Parental Cells
Organism Homo sapiens
Characteristics cell type: HAP1 cells derived from male CML cell line KBM7
morphology: Fibroblast-like
genotype: Wild-type
chip antibody: None
replicate: r2
Treatment protocol Cells were harvested by trypsinization and fixed in suspension with 1% formaldehyde for 10 min at room temperature. The crosslinking reaction was quenched with 125 mM glycine for 5 min, followed by two washes with ice-cold PBS.
Growth protocol Human HAP1 WT and DSETX cells were cultured in IMDM (ThermoFisher) supplemented with 10% FBS (Sigma-Aldrich) and 1% Penicillin/Streptomycin (Sigma-Aldrich). Cells were grown at 37°C and in a humidified atmosphere containing 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Cells were lysed in ChIP cell lysis buffer (5 mM HEPES pH 8.0, 85 mM KCl, 0.5% NP-40 and protease inhibitors) and incubated 5 min on ice. Nuclei were pelleted by centrifugation at 3,900 g for 5 min at 4°C. Nuclei were then resuspended in ChIP nuclear lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS and protease inhibitors) and sheared to fragments between 200-500 bp using a bioruptor sonication system (Diagenode). Sonicated chromatin was clarified by centrifugation at 20,000 g for 15 min at 4°C. The clarified chromatin was incubated with the RNAPII (4H8) antibody-conjugated Protein A Dynabeads (Invitrogen, ThermoFisher) overnight at 4°C.
Libraries were prepared according to Illumina's instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Sequenced reads were aligned against human genome version hg19 using BWA-MEM v0.7.15.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated by converting BAM files to bedGraph format using bedtools' genomeCoverageBed function. bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package. Unscaled read depth coverage over is presented.
 
Submission date Jan 13, 2020
Last update date Apr 29, 2021
Contact name Steve West
E-mail(s) stephen.west@crick.ac.uk
Organization name The Francis Crick Institute
Street address 1 Midland Road
City London
ZIP/Postal code NW1 1AT
Country United Kingdom
 
Platform ID GPL18573
Series (2)
GSE143558 Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2 [ChIP-seq]
GSE143574 Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2
Relations
BioSample SAMN13836880
SRA SRX7547578

Supplementary file Size Download File type/resource
GSM4261890_input.wt.r2.bigwig 263.0 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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