|
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.
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|
|
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 |