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Sample GSM5849885 Query DataSets for GSM5849885
Status Public on May 23, 2024
Title RNA-seq data for sample tumor T839
Sample type SRA
 
Source name D345T2
Organism Homo sapiens
Characteristics tissue: Bladder carcinoma tumor
tumor name in article: T839
Stage: MIBC
mibc consensus classification (rnaseq): LumU
Extracted molecule total RNA
Extraction protocol Tumours RNA were extracted using Triple extraction protocol
The pool of libraries was quantified using a qPCR method (KAPA library quantification kit, Roche). The sequencing was carried out using paired-end mode (PE100) on a Illumina Novaseq 6000 instrument, using a custom primer (provided into the Nugen kit) to initiate the Read 1 sequencing. The target number of reads was about 50 million paired-reads per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Protocol : Nugen Ovation Solo
NovaSeq - S1 - PE100
aligner : STAR
Data were integrated using Deseq2 default parameters and VST normalisation.
Genome_build: human hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include Deseq2 values for all samples (sample as column)
 
Submission date Jan 31, 2022
Last update date May 23, 2024
Contact name Elodie chapeaublanc
E-mail(s) elodie.chapeaublanc@pasteur.fr
Organization name Institut Curie
Department UMR 144
Lab Equipe Radvanyi
Street address 26 rue d'ulm
City paris
ZIP/Postal code 75248
Country France
 
Platform ID GPL24676
Series (1)
GSE195768 RNA-seq Series of Bladder Carcinoma Tumors
Relations
BioSample SAMN25513282
SRA SRX13993825

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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