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| Status |
Public on Sep 30, 2020 |
| Title |
Genome-wide detection of DNA double-strand breaks by in-suspension BLISS |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Other
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| Summary |
sBLISS (in-suspension Break Labeling In Situ and Sequencing) is a versatile and widely applicable method for identification of endogenous and induced DNA double-strand breaks (DSBs), in any cell type that can be brought into suspension. After in situ labeling, DSB ends are linearly amplified followed by next-generation sequencing and DSB landscape analysis. Here, we present a step-by-step experimental protocol for sBLISS, followed by a basic computational analysis. The main advantages of sBLISS are (i) the suspension setup, which circumvents the need to work with delicate coverslips as in the original BLISS, (ii) the possibility for adaptation to a high-throughput robotics or single-cell workflow, and (iii) its flexibility and applicability to virtually every cell type, including patient-derived cells, organoids, and isolated nuclei. The wet-lab protocol can be completed in 1.5 weeks, and it is suitable for researchers with intermediate expertise in molecular biology and genomics. For the computational analyses, basic-to-intermediate bioinformatics expertise is required.
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| Overall design |
Step-by-step protocol for genome-wide DSB labeling using our newly developed sBLISS method. Deposited data (one mouse tissue-sorted jejunum enterocytes, and one human cancer cell experiment set-TK6 cells treated with etoposide or not) aims to provide examples and can be used to work through the included mapping pipeline and analysis tutorial.
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| Contributor(s) |
Bouwman BA, Agostini F, Garnerone S, Petrosino G, Gothe HJ, Sayols S, Moor AE, Itzkovitz S, Bienko M, Roukos V, Crosetto N |
| Citation(s) |
33139954 |
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| Submission date |
Feb 20, 2020 |
| Last update date |
Dec 30, 2020 |
| Contact name |
Federico Agostini |
| E-mail(s) |
agostini.federico@gmail.com
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| Organization name |
Science for Life Laboratories
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| Street address |
Tomtebodavägen 23a
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| City |
Solna |
| State/province |
Stockholm |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA607701 |
| SRA |
SRP250106 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE145598_RAW.tar |
290.3 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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