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Sample GSM3566554 Query DataSets for GSM3566554
Status Public on Sep 01, 2022
Title HAP1_ATAC-seq_WT_CHAF1A_Hairpin3_R1
Sample type SRA
 
Source name cell line
Organism Homo sapiens
Characteristics library: ATAC-seq
cell line: HAP1
replicate: 1
knockout: WT
knockdown: CHAF1A
Growth protocol HAP1 WT and knock-out cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Thermo Fisher Scientific, 21980-032) supplemented with 10% heat inactivated Fetal Bovine Serum (FBS, Thermo Fisher Scientific, 10500) and 1% Pen Strep (100 units/ml Penicillin, 100 µg/ml Streptomycin, Thermo Fisher Scientific, 15140-122). A549 cells were cultured in F-12K Nut Mix (Thermo Fisher Scientific, 21127-022) supplemented with 10% FBS and 1% Pen Strep.
Extracted molecule genomic DNA
Extraction protocol 50000 cells were resuspended in 25 µl transposase reaction mix (0.05% digitonin, 1x TD buffer, 0.08% TDE1 (Nextera DNA Library Preparation Kit, Illumina, FC-121-1031)) and incubated for 30 min, 37°C, 300 rpm. Then DNA was purified using MinElute kit (Qiagen, 28004) and eluted in 11 µl elution buffer. 1 µl was used to determine cycle number for PCR using a qPCR approach. The remaining 10 µl were complemented with 1x NEBnext High-Fidelity PCR master mix (New England BioLabs, M0541), 1.25 µM index primer 1 and 1.25 µM index primer containing a barcode. PCR was performed: 5 min 72°C, 30 sec 98°C, X cycles of 10 sec 98°C + 30 sec 63°C + 1 min 72°C, 1 min 72°C and then cleaned-up using Agencourt AMPure XP beads (Beckman Coulter, A63880).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description ATAC-seq for wild type HAP1 cell line with shRNA against CHAF1A hairpin 3, replicate 1
Data processing Sequenced reads were trimmed for adaptor sequences with Skewer
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
ATAC-seq read coverage at every reference genome position using BEDTools coverage and divided by the total number of reads, converted into bedgraph files and subsequently to bigwig format using bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: Narrow peak files have MACS2 peak calls, BigWig files have read counts per million mapped reads
 
Submission date Jan 17, 2019
Last update date Sep 01, 2022
Contact name Christoph Bock
E-mail(s) cbock@cemm.oeaw.ac.at
Organization name CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platform ID GPL20301
Series (2)
GSE125220 Histone chaperone CAF-1 is a synthetic lethal vulnerability in the context of ARID1A deficiencies [ATAC-Seq]
GSE125221 Histone chaperone CAF-1 is a synthetic lethal vulnerability in the context of ARID1A deficiencies
Relations
BioSample SAMN10764570
SRA SRX5258434

Supplementary file Size Download File type/resource
GSM3566554_HAP1_ATAC-seq_WT_CHAF1A_Hairpin3_R1.bigWig 360.7 Mb (ftp)(http) BIGWIG
GSM3566554_HAP1_ATAC-seq_WT_CHAF1A_Hairpin3_R1.peaks.narrowPeak.gz 1.1 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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