|
| Status |
Public on Apr 15, 2019 |
| Title |
WM164 high HDAC8 |
| Sample type |
SRA |
| |
|
| Source name |
melanoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: WM164
cell type: Melanoma cell line
genotype/variation: BRAF V600E mutation
hdac8 expression: High
|
| Treatment protocol |
No treatment was applied.
|
| Growth protocol |
Cells were grown in RPMI media containing 5% FBS. Cells were seeded at 500,000 cells per 100 cm plate for 48 hours (60-70% confluency).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed with Trizol and RNA was isolated with chloroform. RNA was cleaned up using a Qiagen RNeasy kit.
One hundred nanograms of RNA were then processed for RNA-sequencing using the NuGen Ovation Universal RNA-Seq (San Carlos, CA) following manufacturer’s instructions. Libraries’ qPCR-based quantitation was performed with the Kapa Library Quantification Kit, the libraries were sequenced on the Illumina NextSeq 500 sequencer with a 75-base paired-end run which generated 30-40 million read pairs per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
02_3743040_WM164 HDAC8 OE
processed data file: rnaseq_processed.txt
|
| Data processing |
Log2 transformation was applied to RNA-Seq after examining histograms and boxplots of gene expression across samples. Gene/probesets with undetected gene expression across all samples were excluded from the analyses.
Moderated t-statistics were used to compare the RNA expression between baseline (EV) and HDAC8 overexpression (HDAC8) samples in RNA-seq data for each of 18,452 genes using the limma package in R. After fitting a linear model, this package uses a simple empirical Bayes procedure to moderate the standard errors across genes.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: rnaseq_processed.txt: Tab-delimited text file containing gene symbols (first column) and log2 expression for the four samples (columns two through five).
|
| |
|
| Submission date |
Feb 28, 2019 |
| Last update date |
Apr 15, 2019 |
| Contact name |
Marco Davila |
| E-mail(s) |
marco.davila@moffitt.org
|
| Organization name |
Moffitt Cancer Center
|
| Street address |
12902 USF MAGNOLIA DRIVE, MRC2
|
| City |
TAMPA |
| State/province |
Florida |
| ZIP/Postal code |
33612 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE127564 |
Overexpression of HDAC8 establishes a unique gene signature in BRAF-mutant melanoma cells |
|
| Relations |
| BioSample |
SAMN11038766 |
| SRA |
SRX5446046 |
