|
| Status |
Public on May 23, 2024 |
| Title |
RNA-seq data for sample tumor T877 |
| Sample type |
SRA |
| |
|
| Source name |
D345T3
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bladder carcinoma tumor
tumor name in article: T877
Stage: MIBC
mibc consensus classification (rnaseq): LumNS
|
| 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 |
SAMN25513281 |
| SRA |
SRX13993826 |
