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| Status |
Public on Jul 07, 2020 |
| Title |
Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells (RNA-seq) |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
For the RNAseq experiment: total RNA was isolated from 3 biological replicates of shCTRL-AB22 cells and 3 biological replicates of shHMGB1-AB22 cells. for ATACseq experiment: 1 sample of shCTRL-AB22 cells is compared with 1 sample of shHMGB1-AB22 cells. for BLISS experiment: BLISS libraries are prepared from either shCTRL or shHMGB1-AB22 cells treated with 0, 3, 5 or 10 Gy of gamma-radiations. Each condition is represented with 2 biological replicates.
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| Contributor(s) |
Garcia-Manteiga JM, Brambilla F, Bianchi ME, Agresti A |
| Citation(s) |
32710624 |
| |
| Submission date |
Jul 24, 2019 |
| Last update date |
Oct 06, 2020 |
| Contact name |
Jose Manuel Garcia-Manteiga |
| E-mail(s) |
garciamanteiga.josemanuel@hsr.it
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| Organization name |
OSR - San Raffaele Scientific Institute
|
| Department |
Center for Translational Genomics and Bioinformatics
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| Street address |
Via Olgettina 58
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| City |
Milan |
| State/province |
-- |
| ZIP/Postal code |
20132 |
| Country |
Italy |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE134798 |
Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells |
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| Relations |
| BioProject |
PRJNA556431 |
| SRA |
SRP216244 |
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