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| Status |
Public on Aug 04, 2018 |
| Title |
Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Other
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| Summary |
Single-stranded DNA breaks (nicks) were tagged by biotin-dCTP in wild-type budding yeast cells and mapped by nick-ChIP coupled to whole-genomic microarrays.
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| Overall design |
Live budding yeast cells were fixed by 1% formaldehyde and encapsulated into low-melting point agarose plugs. After cell lysis, free 3'-OH DNA termini were tagged by limited in situ nick translation using E Coli DNA pol I holoenzyme, incorporating bioin-dCTP. As a positive control of nick labeling, part of the samples were treated by nickase enzyme introducing site-specific exogenous ss breaks (nickase-treated samples). Nucleic acid was from control and nickase-treated samples and purified and fragmented by sonication (to an average size of 300-500 bp) and immunoprecipitated by anti-biotin monoclonal antibodies (Sigma). After WGA (whole genome amplification) input samples were lablelled by Cy3, IP sample were labelled by Cy5 and were co-hybridized to 4x44k Agilent microarrays.
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| Contributor(s) |
Székvölgyi L, László H |
| Citation(s) |
30445637 |
| Submission date |
Feb 06, 2018 |
| Last update date |
Nov 30, 2018 |
| Contact name |
Halasz Laszlo |
| E-mail(s) |
hlsz.laszlo@gmail.com
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| Organization name |
University of Debrecen
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| Department |
Department of Biochemistry and Molecular Biology
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| Street address |
Egyetem tér 1
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| City |
Debrecen |
| ZIP/Postal code |
4032 |
| Country |
Hungary |
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| Platforms (1) |
| GPL4131 |
Agilent-014810 Yeast Whole Genome ChIP-on-Chip Microarray 4x44K (G4493A) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA433189 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE110218_Nick.wig.gz |
366.1 Kb |
(ftp)(http) |
WIG |
| GSE110218_Nick_peak.bed.gz |
1.8 Kb |
(ftp)(http) |
BED |
| GSE110218_Nickase.wig.gz |
374.0 Kb |
(ftp)(http) |
WIG |
| GSE110218_Nickase_peak.bed.gz |
3.1 Kb |
(ftp)(http) |
BED |
| GSE110218_RAW.tar |
37.3 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
| Processed data are available on Series record |
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