|
Status |
Public on Apr 28, 2012 |
Title |
mm2 |
Sample type |
SRA |
|
|
Source name |
primary melanoma #1
|
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 |
SRX101664 |
BioSample |
SAMN00739925 |