GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE78172 Query DataSets for GSE78172
Status Public on Jul 18, 2016
Title DSBCapture: in situ capture and direct sequencing of dsDNA breaks
Organism Homo sapiens
Experiment type Other
Expression profiling by high throughput sequencing
Summary 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.
Overall design 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.
Contributor(s) Lensing S, Marsico G, Hansel-Hertsch R, Tannahill D, Balasubramanian S
Citation(s) 27525976, 37095580
Submission date Feb 22, 2016
Last update date May 12, 2023
Contact name Giovanni Marsico
Organization name CRUK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
Platforms (2)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (11)
GSM2068753 EcoRV_restriction_enzyme
GSM2068754 AID-DlvA_AsiSI_restriction_enzyme
GSM2068755 NHEK_break_seq_rep1
BioProject PRJNA312824
SRA SRP070660

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
GSE78172_AsiSI.tar.gz 80.7 Kb (ftp)(http) TAR
GSE78172_BLESS_n1.tdf 1.4 Gb (ftp)(http) TDF
GSE78172_BLESS_n2.tdf 613.0 Mb (ftp)(http) TDF
GSE78172_BREAK.marked.cleaned.fixed.first.sort.subset.tdf 390.2 Mb (ftp)(http) TDF
GSE78172_BREAK.marked.cleaned.fixed.first.sort.tdf 408.5 Mb (ftp)(http) TDF
GSE78172_BREAK_n1.tdf 1.7 Gb (ftp)(http) TDF
GSE78172_BREAK_n2.tdf 1.5 Gb (ftp)(http) TDF
GSE78172_Break_primary_20ug.N1.subset.NOdups.q005_peaks.narrowPeak.gz 2.3 Mb (ftp)(http) NARROWPEAK
GSE78172_ENCODE_peaks.tar.gz 17.9 Mb (ftp)(http) TAR
GSE78172_Eco.first_nodup.cov.bed.gz 5.7 Mb (ftp)(http) BED
GSE78172_NHEK.tar.gz 11.8 Mb (ftp)(http) TAR
GSE78172_RAW.tar 11.9 Gb (http)(custom) TAR (of BEDGRAPH)
GSE78172_all_hek_gibco.avg.txt.gz 90.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap