|
Status |
Public on Apr 15, 2019 |
Title |
1205Lu low HDAC8 |
Sample type |
SRA |
|
|
Source name |
melanoma cell line
|
Organism |
Homo sapiens |
Characteristics |
cell line: 1205Lu cell type: Melanoma cell line genotype/variation: BRAF V600E mutation hdac8 expression: Low
|
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.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
04_43749027_1205Lu 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).
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|
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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 |
SAMN11038765 |
SRA |
SRX5446047 |