|
Status |
Public on Dec 16, 2014 |
Title |
M263_DMSO |
Sample type |
SRA |
|
|
Source name |
Melanoma
|
Organism |
Homo sapiens |
Characteristics |
cell type: Melanoma cell line: M263
|
Treatment protocol |
Cells have been treated with DMSO for 48 hours.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Read mapping was performed using TopHat version 2.0.9 with the NCBI Build 37 reference genome. Read counts per gene were quantified using HTSeq version 0.5.4. The CQN R Package was used to compute FPKM by adjusting read counts for gene length and GC content and to obtain offsets for normalization and analysis using the DESeq2 R package. Genome_build: NCBI Genome build 37 Supplementary_files_format_and_content: Matrix of gene expression measurements in FPKM
|
|
|
Submission date |
Oct 20, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Jennifer Tsoi |
E-mail(s) |
JTsoi@mednet.ucla.edu
|
Organization name |
UCLA
|
Department |
University of California, Los Angeles
|
Lab |
Thomas Graeber
|
Street address |
570 Westwood Blvd, CNSI 4338
|
City |
Los Angeles |
State/province |
CA |
ZIP/Postal code |
90095 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE62526 |
Gene expression profiling of melanoma cell lines by high throughput sequencing |
|
Relations |
BioSample |
SAMN03120884 |
SRA |
SRX736511 |