|
| Status |
Public on Mar 21, 2024 |
| Title |
SCMC_neopetrotaurine_B_7uM_6h |
| Sample type |
SRA |
| |
|
| Source name |
muscle
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: muscle
cell line: SCMC
cell type: Rhabdomyosarcoma
genotype: wt
time: 6 hr
treatment: Neopetrotaurine B
|
| Treatment protocol |
Cells were treated with either DMSO or compound of interest for 6 hours.
|
| Growth protocol |
Cells were maintained in DMEM with 10% FBS and Penn/Strep at 37 °C incubation.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Bulk RNA is extracted using QIAGEN Rneasy Plus Mini Kit.
Illumina TruSeq Stranded mRNA and Total RNA library prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RNA-seq was mapped using STAR with hg19 as reference.
RNA-seq read abundance for each gene counted (TPM) using RSEM
RNA-seq raw reads normalized using DESeq2
Assembly: hg19/GRCh37
Supplementary files format and content: RNA-seq processed files are quantification matrices of TPM (transcripts per million) at the gene level.
|
| |
|
| Submission date |
Dec 05, 2023 |
| Last update date |
Mar 21, 2024 |
| 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 (1) |
| GSE249431 |
Neopetrotaurines A-C, Isoquinoline Alkaloids with an Unprecedented Taurine-Bridged Isoquinoline Quinone Moiety from the Sponge Neopetrosia sp. |
|
| Relations |
| BioSample |
SAMN38689970 |
| SRA |
SRX22795366 |
