|
| Status |
Public on Apr 27, 2017 |
| Title |
RH4 DMSO 6hr RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
RMS cell line, PAX3-FOXO1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RH4
cell type: rhabdomyosarcoma
treatment time: 6 hours
treatment: DMSO
|
| Treatment protocol |
Drug was dissolved in DMSO to a stock conentration of 10 mM, and additionally diluted in DMEM to a final concentration of 500 nM (or DMSO of equivilent final volume), exposing cells for 6 hours before extracting RNA. For shRNA inducible experiments, cells were treated for 48 hours with doxycyclin (100 ng/mL).
|
| 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 RMS cell lines, RH4 and RH41 treated with DMSO or JQ1 for 6 hours, or inducible shRNA derived RH4 cells, using the RNeasy mini kit (Qiagen).
Standard Illumina barcodes were introduced during library preparation
|
| |
|
| 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 |
Jun 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ashish Lal |
| E-mail(s) |
ashish.lal@nih.gov
|
| Phone |
2407607396
|
| 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) |
| GSE83724 |
PAX3-FOXO1 requires BRD4 to drive oncogene addiction in RMS cells [RNA-seq] |
| GSE83728 |
Epigenetic Lanscape and BRD4 Transcriptional Dependency of PAX3-FOXO1 Driven Rhabdomyosarcoma |
|
| Relations |
| BioSample |
SAMN05293630 |
| SRA |
SRX1878932 |
