|
| Status |
Public on Feb 07, 2024 |
| Title |
ish2-CD73-3-No-Dox |
| Sample type |
SRA |
| |
|
| Source name |
RD cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: No-Dox
genotype: Control
cell line: RD
cell type: Rhabdomyosarcoma cell
|
| Treatment protocol |
The cells were treated with or without 10ng/mL of doxycycline. Untreated cells were used as control. The cells were incubated in the treatment for 96hr prior to RNA extraction.
|
| Growth protocol |
5x10^5 cells were seeded in a 6-well plate with 2ml of 10% TET system media and allowed to attach for 24hr.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected in 500µl of TRIzol. Chloroform extraction was performed. Then the aqueous phase was mixed with an equal volume of 75% ethanol and further purified using a RNeasy Mini Kit (QIAGEN, 74104) according to the manufacturer’s protocol. An Agilent 2100 TapeStation was used for RNA quality analysis.
Stranded mRNA-Seq libraries were generated using a KAPA mRNA HyperPrep Kit (Roche, KK8581) following manufacturer’s protocol. Sequencing was performed on an Illumina NextSeq 550 system using a 75-bp, high-output sequencing kit for paired-end sequencing.
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Adaptors were trimmed using Trim Galore (v0.6.4). The trimmed reads were then aligned to the human genome (GRCH38) using STAR (2.7.3a). The subsequent mapped reads were quantified by featureCounts of the Subread (v1.6.3) package.
Assembly: GRCH38
Supplementary files format and content: gene.count.txt
|
| |
|
| Submission date |
Aug 11, 2023 |
| Last update date |
Feb 07, 2024 |
| Contact name |
Lei Guo |
| E-mail(s) |
[email protected]
|
| Phone |
7018859551
|
| Organization name |
University of Texas Southwestern Medical Center
|
| Department |
Department of Population and Data Sciences
|
| Lab |
Lin Xu
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75206 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE240722 |
CD73 contributes to the pathogenesis of Fusion-Negative Rhabdomyosarcoma through the purinergic signaling pathway |
|
| Relations |
| BioSample |
SAMN36949995 |
| SRA |
SRX21346054 |
