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| Status |
Public on Dec 22, 2014 |
| Title |
Genomewide analysis of the human p53 transcriptional network unveils a lncRNA tumor suppressor signature (RNA-seq) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We report the application of high-throughput sequencing to performed the p53 regulated trancriptome in HCT116 colon cancer cells treated with the DNA damage 5FU. To study the direct targets of p53 we performed ChIP-seq to deterrmined the p53 biding sites and associated with the expression levels. With this study we identified the new genomic regions regulated by p53 and with special attention in those regions that are non coding and are differentially expressed by the DNA damage drug.
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| Overall design |
Description of the p53 transcriptome in HCT116 colon cancer cell line. The RNA-seq libraries were prepared from purified poly-A+ RNA from untreated and 5-Fluorouracil treated p53 +/+ HCT116 cells for 4 and 12h, including two independent samples for the time 12h. Paired-end and strand specific RNA sequencing libraries were prepared according to Illumina instructions and sequenced on HiSeq 2000 (Ilumina) with sequence length of 150 bp. Raw sequencing data were alignment to the human genome (hg19) using Tophat mapper.
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| Contributor(s) |
Huarte M, Sanchez Y, Segura V |
| Citation(s) |
25524025 |
| |
| Submission date |
Jun 15, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Maite Huarte |
| E-mail(s) |
maitehuarte@unav.es
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| Organization name |
CIMA
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| Street address |
c/ Avd Pio XII, 55
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| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31008 |
| Country |
Spain |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE58528 |
Genomewide analysis of the human p53 transcriptional network unveils a lncRNA tumor suppressor signature |
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| Relations |
| BioProject |
PRJNA252833 |
| SRA |
SRP043273 |
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