|
| Status |
Public on Apr 13, 2023 |
| Title |
Vehicle_r4 |
| Sample type |
SRA |
| |
|
| Source name |
PDX
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
xenotransplanted cells: ScaBER
cell line origin: human bladder cancer
strain: Hsd:Athymic Nude-Foxn1nu
treatment: 14 days vehicle (0.5% methylcellulose, 0.1% Tween80)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from frozen tissues and cultured cells using TRItidyG (A4051 PanReac AppliChem) . Reverse transcription was performed using TaqMan Reverse Transcription Reagents (ThermoFisher Scientific, N8080234).
Libraries for sequencing were constructed using the QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina protocol | Lexogen and sequenced using the 75-bp protocol on a NextSeq500 (Illumina, San Diego, CA, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Poli A and adapters sequences were cleaned using bbduk software
Nextpresso pipeline was used to carry out the analysis
Alignment performed using TopHat aligner
Gene count matrices were produced using htseqcount
Assembly: mm10 and hg19
|
| |
|
| Submission date |
Nov 22, 2022 |
| Last update date |
Apr 13, 2023 |
| Contact name |
Jaime Martinez de Villarreal |
| E-mail(s) |
jmartinezv@cnio.es
|
| Phone |
+34 917328000
|
| Organization name |
CNIO
|
| Department |
Molecular Oncology Programme
|
| Lab |
Epithelial Carcinogenesis Group
|
| Street address |
Melchor Fernández Almagro, 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL19415 |
| Series (1) |
| GSE218575 |
Transcriptomic analysis of Nintedanib, Alpelisib and Nintedanib;Alpelisib treated bladder tumors |
|
| Relations |
| BioSample |
SAMN31840403 |
| SRA |
SRX18352742 |
