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Series GSE248980 Query DataSets for GSE248980
Status Public on Nov 30, 2023
Title Chromatin context-dependent effects of epigenetic drugs on CRISPR-Cas9 editing
Organism Homo sapiens
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary We sought to find if epigenetic drugs had chromatin context-dependent effects on CRISPR-Cas9 efficiency and DNA double-strand break repair. We performed a multiplexed drug screen in a reporter cell line containing 19 sequencing based pathway reporters. This submission contains high throughput sequencing data of the pathway reporters, their mapping and mutation readout. It also contains the raw pA-DamID data for H3K27me3, H3K9me2, H3K9me3 and "Dam-only" samples in RPE-1 cells.
 
Overall design The samples are pA-DamID experiments, as described in (van Schaik , 2022), where DNA-protein interactions are measured. Here we profile H3K27me3, H3K9me2, H3K9me3 and Dam only in hTERT RPE-1 cells. The Dam only samples are used as controls for DNA accessibility. These data were used in this study to compare DNA repair outcomes of DNA double strand breaks in different chromatin states in RPE-1.

ChIP-seq experiments have been performed using H3K27ac and H3K27me3 antibodies. 3 biological replicates are provided.
 
Citation(s) 38953163
BioProject PRJNA960840
Submission date Nov 29, 2023
Last update date Sep 30, 2024
Contact name Ruben Schep
Organization name Netherlands Cancer Institute
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066CX
Country Netherlands
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (40)
GSM7924237 hTERT RPE-1 pA-DamID gatc counts for H3K27me3 replicate r4
GSM7924238 hTERT RPE-1 pA-DamID gatc counts for H3K27me3 replicate r5
GSM7924239 hTERT RPE-1 pA-DamID gatc counts for H3K27me3 replicate r8

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE248980_K562_H3K27ac_DMSO_merged_bs10.bw 299.4 Mb (ftp)(http) BW
GSE248980_K562_H3K27ac_PCI_merged_bs10.bw 294.6 Mb (ftp)(http) BW
GSE248980_K562_H3K27ac_Tuba_merged_bs10.bw 306.1 Mb (ftp)(http) BW
GSE248980_K562_H3K27me3_DMSO_merged_bs10.bw 424.2 Mb (ftp)(http) BW
GSE248980_K562_H3K27me3_PCI_merged_bs10.bw 439.4 Mb (ftp)(http) BW
GSE248980_K562_H3K27me3_Tuba_merged_bs10.bw 471.7 Mb (ftp)(http) BW
GSE248980_RAW.tar 3.5 Gb (http)(custom) TAR (of BROADPEAK, BW, NARROWPEAK, TXT)
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Raw data are available in SRA
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