|
| Status |
Public on Dec 16, 2014 |
| Title |
M238_DMSO |
| Sample type |
SRA |
| |
|
| Source name |
Melanoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Melanoma
cell line: M238
|
| 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 |
SAMN03120887 |
| SRA |
SRX736507 |
