Transcriptomics

Dataset Information

340

DSBCapture: in situ capture and direct sequencing of dsDNA breaks


ABSTRACT: Double-strand DNA breaks (DSBs) continuously arise and are a source of mutations and chromosomal rearrangements. Here, we present DSBCapture, a sequencing-based method that captures DSBs in situ and directly maps these at single nucleotide resolution enabling the study of DSB origin. DSBCapture shows substantially increased sensitivity and data yield compared to other methods. Employing DSBCapture, we uncovered a striking relationship between DSBs and elevated transcription within nucleosome-depleted chromatin. 6 library samples, 75 base pairs (50 bp for the EcoRV library) custom protocol (DSBCapture or BLESS) sequenced as paired-end reads on Illumina NextSeq 500 (MiSeq for EcoRV library): 1 replicate for the EcoRV library, 1 replicate for the library coming from the U2OS AID-DlvA cell line with AsiSI restriction enzyme, 2 replicates for the BREAk-seq NHEK libraries and 2 replicates for the BLESS NHEK libraries. 4 RNA-Seq library samples from HEK Gibco cells, single-end sequencing on the Illumina NextSeq 500, 75 base pairs.

ORGANISM(S): Homo sapiens  

SUBMITTER: David Tannahill   Shanakr Balasubramanian  Stefanie Lensing  Robert Hansel-Hertsch  Giovanni Marsico 

PROVIDER: E-GEOD-78172 | ArrayExpress | 2016-07-18

SECONDARY ACCESSION(S): SRP070660GSE78172PRJNA312824

REPOSITORIES: GEO, ArrayExpress, ENA

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