|
| Status |
Public on May 29, 2019 |
| Title |
RH41 MC1568 high |
| Sample type |
SRA |
| |
|
| Source name |
FP-RMS cell line, PAX3-FOXO1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RH4
cell type: FP-RMS cell line
treatment time: 6 hours
treatment: MC 1568 10 uM
drug target: HDAC4/5
|
| Treatment protocol |
Drug was dissolved in DMSO to a stock concentration of 10 mM, and additionally diluted in DMEM to a final concentration of 0.5, 1, 5, or 10 µM (or DMSO of equivalent final volume), exposing cells for 1, 6 or 24 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 FP-RMS cell lines 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 |
| |
|
| Description |
Paired-end
|
| Data processing |
RNA-seq reads were aligned to the hg19 reference genome using STAR.
Gene expression values were calculated as Transcripts per Million (TPM) using STAR and the UCSC reference at the gene level.
Differential gene expression was determined using EdgeR.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: TPM files are provided in txt format at the gene-level.
|
| |
|
| Submission date |
Oct 10, 2018 |
| Last update date |
May 30, 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) |
| GSE120771 |
Selective Disruption of Core Regulatory Transcription |
| GSE121106 |
Selective Disruption of Core Regulatory Transcription [RNA-seq] |
|
| Relations |
| BioSample |
SAMN10229563 |
| SRA |
SRX4831254 |
