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Series GSE201829 Query DataSets for GSE201829
Status Public on Jul 15, 2022
Title Genome-wide analysis of DSBs sites in HEK293T cells
Organism Homo sapiens
Experiment type Other
Summary For genome-wide identification and analysis of endogenous DSBs in HEK293T cells chromosomes the ligation-mediated PCR and deep sequencing of the DSBs library were used. The cells were included in low-melt agarose, and the plugs were used for isolation of DNA in a solid phase using incubation in the solution containing 0.5 M EDTA (pH 9.5), 1% sodium laurylsarcosine, and 1-2 mg of proteinase K per ml for 40-48 hr at 50°C. Then DNA was isolated by electro-elution and used for ligation with biotinylated ds-adapter. To shorten large DNA molecules the digestion with Sau3A endonuclease was performed. Then the short regions of DNA attached to DSBs sites were selected using the streptavidin magnespere paramagnetic particles. To prepare samples for amplification of DSBs library the Sau3A adapter was ligated at the opposite to DSBs sites. PCR amplification was performed using the primers corresponding to biotinylated and Sau3A adapters. The library was used for paired end sequencing. The corresponding reads were processed and used for analysis of their distribution in human genome.
Overall design Analysis of human epigenome by the genome-wide analysis of DSBs
Contributor(s) Tchurikov NA, Kravatsky YV, Kretova OV
Citation(s) 35806206
Submission date Apr 28, 2022
Last update date Jul 16, 2022
Contact name Nickolai Tchurikov
Organization name Engelhardt Institute of Molecular Biology
Department Department of Epigenetic Mechanisms of Gene Expression Regulation
Street address 32, Vavilova str.
City Moscow
ZIP/Postal code 119991
Country Russia
Platforms (1)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
Samples (2)
GSM6073759 DSB RAFT HEK293T rep1
GSM6073760 DSB RAFT HEK293T rep2
BioProject PRJNA833124

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
GSE201829_DSB_HEK293T_hg19.intersect.bedGraph.gz 26.9 Mb (ftp)(http) BEDGRAPH
GSE201829_DSB_HEK293T_hg19.intersect.noDFAM.txt.gz 44.8 Mb (ftp)(http) TXT
GSE201829_DSB_HEK293T_hg38.intersect.bedGraph.gz 27.5 Mb (ftp)(http) BEDGRAPH
GSE201829_DSB_HEK293T_hg38.intersect.noDFAM.txt.gz 47.1 Mb (ftp)(http) TXT
GSE201829_RAW.tar 515.7 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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