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| Status |
Public on Apr 21, 2013 |
| Title |
Global genomic profiling of p53-regulated genes |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
p53 is a critical tumor suppressor and works as a stress-induced transcription factor to induce target genes mediating apoptosis, cell cycle arrest and senescence or other responses. To gain new insights into p53 biology, we used high-throughput sequencing to analyze global p53 transcriptional networks in primary mouse embryo fibroblasts in response to DNA damage. ChIP-sequencing reveals 4785 p53-bound sites in the genome located near 3193 genes involved in diverse biological processes. RNA-sequencing analysis shows that only a subset of p53-bound genes is transcriptionally regulated, yielding a list of 432 p53-bound and regulated genes. Furthermore, we define a list of 1269 basal-p53 regulated genes, of which 253 are p53-bound and basal-p53 regulated.
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| Overall design |
ChIP-seq was performed to determine the genome-wide p53 binding sites in doxorubicin-treated primary MEFs. RNA-seq was used to define differentially expressed genes in response to DNA damage in wild-type and p53-/- MEFs, and basal p53 regulated genes by deriving differentially expressed genes between untreated wild-type and p53-/- MEFs.
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| |
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| Contributor(s) |
Kenzelmann Broz D, Attardi LD |
| Citation(s) |
23651856, 25704813 |
| |
| Submission date |
Apr 20, 2013 |
| Last update date |
Jul 31, 2019 |
| Contact name |
Stephano Spano Mello |
| Organization name |
Stanford University
|
| Lab |
Attardi lab
|
| Street address |
269 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA198448 |
| SRA |
SRP021219 |
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