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Series GSE139011 Query DataSets for GSE139011
Status Public on Dec 31, 2019
Title Novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary Single strand breaks (SSBs) represent the major form of DNA damage, yet no technique exists to map these lesions genome-wide with nucleotide-level precision. Herein, we present a method, termed SSiNGLe, and demonstrate its utility to explore the distribution and dynamic changes in genome-wide SSBs in response to different biological and environmental stimuli. We validate SSiNGLe using two very distinct sequencing techniques and apply it to derive global profiles of SSBs in different biological states. Strikingly, we show that patterns of SSBs in the genome are non-random, specific to different biological states, enriched in regulatory elements, exons, introns, specific types of repeats and exhibit differential preference for the template strand between exons and introns. Furthermore, we show that breaks likely contribute to naturally occurring sequence variants. Finally, we demonstrate strong links between SSB patterns and age. Overall, SSiNGLe provides access to unexplored realm of cellular biology, not obtainable with current approaches.
 
Overall design Profiling of single-strand DNA breaks in response to anti-cancer drug treatments and in multiple cell types
 
Contributor(s) Cao H, Kapranov P
Citation(s) 31862872
Submission date Oct 17, 2019
Last update date Dec 31, 2019
Contact name Huifen Cao
E-mail(s) hfcao_bnu@163.com, hfcao@hqu.edu.cn
Phone +86 05926167250
Organization name Huaqiao University
Department School of Biomedical Sciences
Lab Institute of Genomics
Street address 668 Jimei Road
City Xiamen
State/province Fujian
ZIP/Postal code 361021
Country China
 
Platforms (2)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (109)
GSM4126100 K562 treated with 10074-G5 for 12 hours bioreplica 1
GSM4126101 K562 treated with 10074-G5 for 12 hours bioreplica 2
GSM4126102 K562 treated with 10074-G5 for 24 hours bioreplica 1
Relations
BioProject PRJNA578070
SRA SRP226036

Download family Format
SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE139011_RAW.tar 542.9 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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