|
Status |
Public on Apr 13, 2023 |
Title |
Vehicle_r2 |
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 |
SAMN31840405 |
SRA |
SRX18352740 |