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Series GSE229874 Query DataSets for GSE229874
Status Public on Apr 17, 2024
Title Genome-wide profiling of DNA repair proteins in single cells
Organism Homo sapiens
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary Accurate repair of DNA damage is critical for maintenance of genomic integrity and cellular viability. Because damage occurs non-uniformly across the genome, single-cell resolution is required for proper interrogation, but sensitive detection has remained challenging. Here, we present a comprehensive analysis of repair protein localization in single cells using DamID and ChIC sequencing techniques. This study reports genome-wide binding profiles in response to DNA double-strand breaks induced by AsiSI, and explores variability in genomic damage locations and associated repair features in the context of spatial genome organization.
By unbiasedly detecting repair factor localization, we find that repair proteins often occupy entire topologically associating domains, mimicking variability in chromatin loop anchoring. Moreover, we demonstrate the formation of multi-way chromatin hubs in response to DNA damage. Notably, larger hubs show increased coordination of repair protein binding, suggesting a preference for cooperative repair mechanisms. Together, our work offers new insights into the heterogeneous processes underlying genome stability in single cells.
 
Overall design Genome-wide profiling of DNA repair protein binding/occupancy by high-throughput sequencing (using DamID and ChIC), characterizing the response to sequence-specific double-strand break induction in U2OS cells.
Single-molecule chromatin conformation profiling by Tri-C and SPRITE.
Web link https://doi.org/10.1101/2023.05.10.540169
 
Contributor(s) de Luca KL
Citation(s) 39572529
Submission date Apr 17, 2023
Last update date Dec 05, 2024
Contact name Kim de Luca
Organization name Hubrecht Institute
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584CT
Country Netherlands
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (55)
GSM7179349 U2OS DIvA exp01 Dam-53BP1 (KIN1554.index01)
GSM7179350 U2OS DIvA exp01 Dam-53BP1 (KIN1554.index02)
GSM7179351 U2OS DIvA exp01 Dam untethered (KIN1554.index03)
Relations
BioProject PRJNA956510

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
GSE229874_MSR20210621.chic_ivs.1000.tsv.gz 57.9 Mb (ftp)(http) TSV
GSE229874_MSR20210621.damid_ivs.1000.tsv.gz 62.4 Mb (ftp)(http) TSV
GSE229874_RAW.tar 98.2 Mb (http)(custom) TAR (of TSV)
GSE229874_scRepair.barcodes.tsv.gz 5.6 Kb (ftp)(http) TSV
GSE229874_scRepair.sample_overview.tsv.gz 114.4 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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