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| 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
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| 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.
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| 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.
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| 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 |
| E-mail(s) |
persego@gmail.com
|
| Organization name |
CRUK Cambridge Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA312824 |
| SRA |
SRP070660 |
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