|
| Status |
Public on Apr 01, 2018 |
| Title |
RD 10 nM Tram, 48 hrs |
| Sample type |
SRA |
| |
|
| Source name |
RMS cell line, mutant NRAS
|
| Organism |
Homo sapiens |
| Characteristics |
treatment time: 48 hours
treatment: 10 nM Trametinib
|
| Treatment protocol |
Drug was dissolved in DMSO to a stock conentration of 10 mM, and additionally diluted in DMEM to a final concentration of 10 or 100 nM (or DMSO of equivilent final volume), exposing cells for 6, 24 or 48 hours before extracting RNA.
|
| Growth protocol |
Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from FN-RMS cell lines using the RNeasy mini kit (Qiagen).
Standard Illumina barcodes were introduced during library preparation
RNA-seq Paired-End
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RNA-seq reads were aligned to the hg19 reference genome using TopHat.
Gene expression values were calculated as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using Cufflinks and the UCSC reference at the gene level.
Differential gene expression was determined using Cuffdiff (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/).
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM files are provided in txt format at the gene-level
|
| |
|
| Submission date |
Aug 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Javed Khan |
| E-mail(s) |
khanjav@mail.nih.gov
|
| Phone |
2407606135
|
| Organization name |
NCI, NIH
|
| Department |
Genetics Branch
|
| Lab |
Javed Khan
|
| Street address |
37 Convent Dr.
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE85170 |
MEK inhibition rewires enhancer landscapes in RAS-driven Rhabdomyosarcoma to unlock a myogenic differentation block |
| GSE85171 |
Epigenetic Reprogramming of mutant RAS-driven Rhabdomyosarcoma via MEK Inhibition |
|
| Relations |
| BioSample |
SAMN05510464 |
| SRA |
SRX1998444 |
