|
| Status |
Public on Apr 28, 2012 |
| Title |
Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration [HT-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Most cancer genomics papers to date have focused on aberrations in genomic DNA and protein-coding transcripts. However, around 50% of transcripts have no coding potential and may exist as non-coding RNA. We performed RNA-seq in BRAFv600e melanoma skin cancer and on melanocytes over-expressing oncogenic BRAF to catalog transcriptome remodeling. We discovered that BRAF regulates expression of 1027 protein coding transcripts, 39 annotated lncRNAs and 70 novel transcripts. Many of the novel transcripts are lncRNAs. We used an indepenedent dataset to interrogate our novel transcripts and found that the novel lncRNA BANCR is a BRAF-regulated lncRNA recurrently upregulated in melanoma. Knockdown of BANCR impairs melanoma cell migration.
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| |
|
| Overall design |
Whole transcriptome RNA-seq followed assembly to Refseq/Gencode and de novo transcript assembly. RNA-seq performed on: 2 BRAFv600e melanomas, melanocytes+RFP control and melanocytes + BRAFv600e. We discovered protein-coding transcripts, annotated ncRNAs and novel transcripts (including lncRNAs) regulated by BRAFv600e also coordinately expressed in melanoma.
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| |
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| Contributor(s) |
Flockhart R, Webster D, Qu K, Mascarenhas N, Kovalski J, Kretz M, Khavari P |
| Citation(s) |
22581800 |
| |
| Submission date |
Oct 19, 2011 |
| Last update date |
Oct 11, 2022 |
| Contact name |
Douglas Porter |
| Organization name |
Stanford
|
| Department |
Dermatology
|
| Lab |
Khavari
|
| Street address |
269 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (4)
|
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| This SubSeries is part of SuperSeries: |
| GSE37169 |
Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration |
|
| Relations |
| SRA |
SRP009029 |
| BioProject |
PRJNA149345 |
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