|
| Status |
Public on Apr 28, 2012 |
| Title |
mm4 |
| Sample type |
SRA |
| |
|
| Source name |
primary melanoma #2
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primary melanoma
|
| Treatment protocol |
Melanocytes were infected with lentivirus transmitting either red fluorescent protein (RFP) control or BRAFv600e. Samples were harvested 3 days after infection for RNA extraction.
|
| Growth protocol |
Melanocytes cultured in melanocyte medium 154 (Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted using RNeasy kit (Qiagen). Poly-A mRNA was selected for and processed using the Illumina RNA sequencing kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA-seq from primary human melanoma sample
|
| Data processing |
Fragment length average = 350bp +/- 50bp
Briefly, Raw reads mapped to hg18 using Tophat. De novo assembly was performed using Scripture. Assembly to Refseq/Gencode was performed using Cufflinks and differential expression was calculated using Cuffdiff.
|
| |
|
| 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 |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE33092 |
Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration [HT-seq] |
| GSE37169 |
Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration |
|
| Relations |
| SRA |
SRX101665 |
| BioSample |
SAMN00739926 |
