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Title: Three-dimensional proximity mapping of the DRGFP DNA double-strand break site in U2OS cells      
dateReleased:
08-22-2014
description:
We mapped the DNA sequences located in physical proximity to an I-SceI endonuclease-dependent DNA double-strand break (DSB) site to be able to study the impact of DSBs on the break-associated chromatin micro-environment. The I-SceI DSB site is part of a DRGFP transgene that serves as a reporter for homology-directed DSB repair and was stably integrated into U2OS human osteosarcoma cells (Pierce et al., Genes Dev, 1999). DRGFP-U2OS cells were modified to carry a stable Doxycycline (Dox)-inducible I-SceI transgene (TRE-I-SceI) as well as the Tet-ON vector from Contech. Circular chromosome conformation capture (4C) was used to identify DSB-proximal DNA. 4C amplified DNA was subjected to Illumina Hi-Seq 200 100 bp paired end sequencing and reads were mapped to the human genome. The resulting genome-wide map of I-SceI/DRGFP-proximal DNA allows for the investigation of changes in DSB-surrounding chromatin features following I-SceI-mediated DSB induction. 4C library of I-SceI (DRGFP)-proximal DNA contacts in DRGFP-U2OS cells was generated using Illumina Hi-Seq 2000 sequencing, data sets are from two independent experiments.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-58563
refinement:
raw
alternateIdentifiers:
58563
keywords:
functional genomics
dateModified:
12-10-2014
availability:
available
types:
gene expression
name:
Homo sapiens
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-58563/E-GEOD-58563.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-58563/E-GEOD-58563.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58563
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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