|
Status |
Public on Apr 13, 2023 |
Title |
BYL_rep2 |
Sample type |
SRA |
|
|
Source name |
PDX
|
Organisms |
Homo sapiens; Mus musculus |
Characteristics |
xenotransplanted cells: VM-CUB-1 cell line origin: human bladder cancer mouse strain: Hsd:Athymic Nude-Foxn1nu treatment: 7 days Alpelisib (25mg/kg)
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Total RNA was isolated from frozen tissues and cultured cells using ReliaPrep RNA Miniprep Systems (Promega, Z6012). Reverse transcription was performed using TaqMan Reverse Transcription Reagents (ThermoFisher Scientific, N8080234). Libraries for whole-transcriptome sequencing were constructed using the TruSeq RNA Sample Preparation Kit v2 and sequenced using the 75-bp paired-end 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 |
Nextpresso pipeline was used to carry out the analysis: Alignment performed using Bowtie and TopHat aligners Counts were generated using htseqcount Normalization and differential expression analysis performed with DEseq2 Genome_build: hg19 and mm10
|
|
|
Submission date |
Aug 26, 2021 |
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) |
GSE182833 |
Transcriptomic analysis of Nintedanib, Alpelisib and Nintedanib;Alpelisib treated bladder tumors |
|
Relations |
BioSample |
SAMN20990062 |
SRA |
SRX11916393 |