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Sample GSM6752772 Query DataSets for GSM6752772
Status Public on Apr 13, 2023
Title Nintedanib_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 Nintedanib (40mg/kg)
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 SAMN31840409
SRA SRX18352736

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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