|
| Status |
Public on Apr 21, 2020 |
| Title |
Genomewide nucleotide-resolution mapping of single-strand breaks and lesions by GLOE-Seq [Human_Ligase_inactivation] |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| 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.
|
| |
|
| Overall design |
V. Analysis of Okazaki fragments and global DNA single-strand breaks in human cells DNA ligase-competent and -compromised HCT116 cells were subjected to GLOE-Seq analysis in two replicates each. Ligase-competent cells were used to map the genomewide distribution of DNA single-strand breaks. Cells with inactivated DNA Ligase 1 and 3 were used to map the distribution of Okazaki fragments.
|
| |
|
| Contributor(s) |
Sriramachandran AM, Petrosino G, Méndez-Lago M, Schäfer A, Batista-Nascimento LS, Zilio N, Ulrich HD |
| Citation(s) |
32320643 |
| |
| Submission date |
Jul 12, 2019 |
| Last update date |
Jun 16, 2020 |
| Contact name |
Helle Ulrich |
| E-mail(s) |
h.ulrich@imb-mainz.de
|
| Organization name |
Institute of Molecular Biology
|
| Street address |
Ackermannweg 4
|
| City |
Mainz |
| State/province |
Germany |
| ZIP/Postal code |
55128 |
| Country |
Germany |
| |
|
| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (8)
|
|
| This SubSeries is part of SuperSeries: |
| GSE134225 |
Genome-wide nucleotide-resolution mapping of DNA replication patterns, single-strand breaks and lesions by GLOE-Seq |
|
| Relations |
| BioProject |
PRJNA554350 |
| SRA |
SRP214484 |
Less...
More...