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Sample GSM5537857 Query DataSets for GSM5537857
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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