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| Status |
Public on Dec 31, 2011 |
| Title |
RIP-chip of HuR in MCF7 cells exposed to doxorubicin |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
The purpose of the study was to identify mRNA bound to HuR in the presence of doxorubicin in MCF7 cells. We collected cytoplasmic RNA from untreated and treated cells and detected differentially expressed genes (DEGs). We also coimmunoprecipitated HuR and IgG (as control) from doxorubicin treated cells. Comparison between HuR RIP and IgG RIP signals was used to discriminate specific mRNA bound to HuR. HuR coimmmunoprecipitated material was hybridized together with cytoplasmic mRNA of doxorubicin treated cells, enabling the fold enrichment calculation and the selection of mRNAs bound to HuR.
Keywords: RIP-Chip, HuR, doxorubicin, MCF7, HuR consensus binding, post-transcriptional regulation.
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| Overall design |
We subjected MCF7 cells to starvation for 24h and then we added doxorubicin at final concentration of 10 uM, profiling before and after 4 hours of treatment in biological quadruplicate (only on cytoplasmic mRNAs, as HuR was found in the cytoplasm). Differentially expressed genes, altered during the treatment, were identified. Data derived from HuR RIP-Chip and IgG RIP-Chip (in biological quadruplicate) allowed the identification of specific mRNAs bound to HuR. The comparison between HuR RIP-Chip and cytoplasmic extracts from doxorubicin treated cells (in biological triplicate) identified those genes that were more strictly bound to HuR independently from their expression levels.
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| Contributor(s) |
Tebaldi T, Latorre E, Spartà AM, Viero G, Quattrone A, Provenzani A |
| Citation(s) |
22436134 |
| Submission date |
Oct 18, 2011 |
| Last update date |
Jan 23, 2019 |
| Contact name |
Toma Tebaldi |
| E-mail(s) |
t.tebaldi@unitn.it
|
| Organization name |
University of Trento
|
| Department |
Centre for Integrative Biology
|
| Street address |
via Sommarive n. 9
|
| City |
Povo |
| State/province |
Trento |
| ZIP/Postal code |
38123 |
| Country |
Italy |
| |
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| Platforms (1) |
| GPL6480 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version) |
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| Samples (11)
|
| GSM818853 |
MCF7 - cyto doxorubicin vs cyto untreated - bio.rep#1 |
| GSM818854 |
MCF7 - cyto doxorubicin vs cyto untreated - bio.rep#2 |
| GSM818855 |
MCF7 - cyto doxorubicin vs cyto untreated - bio.rep#3 |
| GSM818856 |
MCF7 - cyto doxorubicin vs cyto untreated - bio.rep#4 |
| GSM818857 |
MCF7 doxorubicin - Hur RIP-Chip vs IgG RIP-Chip - bio.rep#1 |
| GSM818858 |
MCF7 doxorubicin - Hur RIP-Chip vs IgG RIP-Chip - bio.rep#2 |
| GSM818859 |
MCF7 doxorubicin - Hur RIP-Chip vs IgG RIP-Chip - bio.rep#3 |
| GSM818860 |
MCF7 doxorubicin - Hur RIP-Chip vs IgG RIP-Chip - bio.rep#4 |
| GSM818861 |
MCF7 doxorubicin - Hur RIP-Chip vs cyto - bio.rep#1 |
| GSM818862 |
MCF7 doxorubicin - Hur RIP-Chip vs cyto - bio.rep#2 |
| GSM818863 |
MCF7 doxorubicin - Hur RIP-Chip vs cyto - bio.rep#3 |
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| Relations |
| BioProject |
PRJNA149461 |
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