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| Status |
Public on Apr 21, 2020 |
| Title |
Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [MMS treatment] |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Other
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| Summary |
Numerous methods are available for the mapping of DNA lesions ranging from double-strand breaks (DSBs) to incorporated ribonucleotides. We now present a technology based on the Genomewide Ligation of 3’-OH Ends (GLOE-Seq) and an associated computational pipeline designed for single-stranded breaks (SSBs), but versatile enough to be applied to any lesion that is convertible into a free 3’-OH terminus. We demonstrate its applicability to the mapping of Okazaki fragments without prior size selection and detect biases and asymmetries in the distribution of spontaneous SSBs in budding yeast and human DNA.
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| Overall design |
VI. Genomewide mapping of lesions in DNA following MMS damage in yeast GLOE-Seq was applied to samples of yeast genomic DNA isolated from cells challenged or not with 0.02% MMS, after treatment with hAAG and APE1 for conversion of alkylated bases to nicks. To map the endogenous repair intermediates, the same samples were not subjected to hAAG/APE1 treatment. Two replicates were used per condition.
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| Contributor(s) |
Sriramachandran AM, Petrosino G, Méndez-Lago M, Schäfer A, Batista-Nascimento LS, Zilio N, Ulrich HD |
| Citation(s) |
32320643 |
| |
| Submission date |
Feb 10, 2020 |
| Last update date |
Jun 16, 2020 |
| Contact name |
Helle Ulrich |
| E-mail(s) |
h.ulrich@imb-mainz.de
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| Organization name |
Institute of Molecular Biology
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| Street address |
Ackermannweg 4
|
| City |
Mainz |
| State/province |
Germany |
| ZIP/Postal code |
55128 |
| Country |
Germany |
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| Platforms (1) |
| GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
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| Samples (48)
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| This SubSeries is part of SuperSeries: |
| GSE134225 |
Genome-wide nucleotide-resolution mapping of DNA replication patterns, single-strand breaks and lesions by GLOE-Seq |
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| Relations |
| BioProject |
PRJNA605786 |
| SRA |
SRP247973 |
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