Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide detection of DNA double-strand breaks by in-suspension BLISS

ABSTRACT: Genome-wide detection of DNA double-strand breaks by in-suspension BLISS

PROVIDER: PRJNA607701 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11119500.fastq.gz	Fastqsanger.gz
	SRR11119501.fastq.gz	Fastqsanger.gz
	SRR11119502.fastq.gz	Fastqsanger.gz
	SRR11119503.fastq.gz	Fastqsanger.gz
	SRR11119504.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

Genome-wide detection of DNA double-strand breaks by in-suspension BLISS

Project description: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.

2020-09-30 | GSE145598 | GEO

Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells [BLISS human]

Project description:The number and position of breaks using BLISS-seq was measured in MCF-7 cells upon irradiation with 10 Gy and with or without the use of the antioxidant (N-acetylcysteine, NAC, 10mM).

2020-07-07 | GSE150016 | GEO

Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells (BLISS)

Project description:The depletion of HMGB1 reduces the deposition of histones on naked DNA (Celona et al, 2011). in primary MEFs and yeast. We verified that the downmodulation of HMGB1 decreases histone level also in a model of murine mesothelioma. HMGB1 was KD in Murine Mesothelioma AB22 cells by the expression of a shRNA. Nucleosome positioning and occupancy were tested by ATAC-seq. Since a reduced amount of nucleosomes increase the cell sensitivity to gamma irradiatio, we tested the number and position of breaks using BLISS-seq.

2020-07-07 | GSE134797 | GEO

Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells (BLISS)

Project description:Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells (BLISS)

| PRJNA556433 | ENA

Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts [BLISS]

Project description:Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts [BLISS]

| PRJNA992562 | ENA

Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells [BLISS human]

Project description:Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells [BLISS human]

| PRJNA630892 | ENA

Double-strand breaks in spo11 mutants

Project description:Double-strand breaks in spo11 mutants

| PRJNA631751 | ENA

Doxorubicin induces double-strand breaks at CpG island promoters

Project description:Doxorubicin is a widely used chemotherapeutic drug that intercalates between DNA base-pairs and posions Topoisomerase II, although the mechanistic basis for cell killing remains speculative. Here we show that both anthracyclines and Topoisomerase II poison cause enhanced DNA double-strand breaks around CpG island promoters of active genes genome-wide. We propose that torsion-based enhancement of nucleosome turnover exposes promoter DNA, ultimately causing DNA breaks around promoters that contributes to cell killing. We have analyzed mouse squamous cell carcinoma cells treated with doxorubicin, aclarubicin and etoposide. The direct in situ Breaks Labeling, Enrichment on Streptavidin (BLESS, PMID 23503052) method was used for mapping DNA double-strand breaks genome-wide.

2015-01-31 | E-GEOD-62927 | biostudies-arrayexpress

Genome-wide maps of double-strand breaks

Project description:Genome-wide maps of double-strand breaks

| PRJNA562301 | ENA

Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration [BLISS]

Project description:Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration [BLISS]

| PRJNA945055 | ENA