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Series GSE145598 Query DataSets for GSE145598
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
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.
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.
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
Submission date Feb 20, 2020
Last update date Dec 30, 2020
Contact name Federico Agostini
Organization name Science for Life Laboratories
Street address Tomtebodavägen 23a
City Solna
State/province Stockholm
ZIP/Postal code 171 65
Country Sweden
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (10)
GSM4322057 TK6_DMSO_Rep1
GSM4322058 TK6_ETO_Rep1
GSM4322059 TK6_DMSO_Rep2
BioProject PRJNA607701
SRA SRP250106

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Supplementary file Size Download File type/resource
GSE145598_RAW.tar 290.3 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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