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Series GSE67941 Query DataSets for GSE67941
Status Public on Apr 19, 2015
Title Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution
Organism Homo sapiens
Experiment type Other
Summary We developed a method for genome-wide mapping of DNA excision repair named XR-seq (eXcision Repair-seq). Human nucleotide excision repair generates two incisions surrounding the site of damage, creating a ~30-mer. In XR-seq, this fragment is isolated and subjected to high-throughput sequencing. We used XR-seq to produce stranded, nucleotide-resolution maps of repair of two UV-induced DNA damages in human cells, cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine-pyrimidone photoproducts ((6-4)PPs). In wild-type cells, CPD repair was highly associated with transcription, specifically with the template strand. Experiments in cells defective in either transcription-coupled excision repair or general excision repair isolated the contribution of each pathway to the overall repair pattern, and showed that transcription-coupled repair of both photoproducts occurs exclusively on the template strand. XR-seq maps capture transcription-coupled repair at sites of divergent gene promoters and bi-directional eRNA production at enhancers. XR-seq data also uncovered the repair characteristics and novel sequence preferences of CPDs and (6-4)PPs. XR-seq and the resulting repair maps will facilitate studies of the effects of genomic location, chromatin context, transcription, and replication on DNA repair in human cells.
Overall design We have performed XR-seq for two types of UV-induced damages (CPD and (6-4)PP) in three different cell lines: NHF1, XP-C (XP4PA-SV-EB, GM15983)), and CS-B (CS1ANps3g2, GM16095). Two biological replicates were performed for each experiment, in which independent cell populations were UV treated and subjected to XR-seq.
Contributor(s) Hu J, Adar S, Selby CP, Lieb JD, Sancar A
Citation(s) 25934506, 37844222
Submission date Apr 15, 2015
Last update date Nov 16, 2023
Contact name Sheera Adar
Organization name Hebrew University of Jerusalem
Department Department of Microbiology and Molecular Genetics
Lab Sheera Adar
Street address Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem
City Jerusalem
State/province Israel
ZIP/Postal code 91120
Country Israel
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (12)
GSM1659156 NHF1 CPD XR-seq, rep1
GSM1659157 NHF1 CPD XR-seq, rep2
GSM1659158 NHF1 6-4PP XR-seq, rep1
BioProject PRJNA281260
SRA SRP057214

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Supplementary file Size Download File type/resource 73.5 Mb (ftp)(http) BW 85.9 Mb (ftp)(http) BW 130.6 Mb (ftp)(http) BW 135.1 Mb (ftp)(http) BW 111.9 Mb (ftp)(http) BW 111.7 Mb (ftp)(http) BW 149.1 Mb (ftp)(http) BW 148.8 Mb (ftp)(http) BW 68.7 Mb (ftp)(http) BW 67.6 Mb (ftp)(http) BW 68.5 Mb (ftp)(http) BW 67.4 Mb (ftp)(http) BW
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