|
| Status |
Public on Sep 20, 2023 |
| Title |
mouse, primary RT, 38594A |
| Sample type |
SRA |
| |
|
| Source name |
primary RT
|
| Organism |
Mus musculus |
| Characteristics |
tumor location: intra-cranial, intra-CNS
Sex: not available
age (days): 30
genotype: Smarcb1flox/flox;R26-CreERT2
tissue: primary RT
time point: E6
|
| Growth protocol |
Mice were monitored for tumour formation at least 3 times per week. The observation period encompassed at least 18 months. The animals who showed clinical behaviour (neurologic symptoms or distress) were euthanized, tumours and all organs were taken and fixed in AFA for histology or were frozen in -80°C until RNA extraction.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The tumour RNAs were extracted using a miRNeasy mini kit (Qiagen ref: 217004) according to manufacturer procedure.
Barcoded Illumina compatible libraries were generated from 750 ng of total RNA for each sample using TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, California, U.S.,). Libraries were sequenced using the illumina NovaSeq platform in the 100 bp paired-end mode.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
38594A
|
| Data processing |
Raw data were processed using an in-house pipeline developed at the Institut Curie Bioinformatics Core Facility, following standard analysis in the field and available at https://github.com/bioinfo-pf-curie/RNA-seq.
Sequencing adaptors were trimmed using TrimGalore!
read QC were performed using fastqc
read mapping on mm10 reference genonme were performed using STAR (version 2.5.3a) and the refFlat gene annotation downloaded from UCSC
duplicated reads were marked with picard and removed
Assembly: mm10
Supplementary files format and content: a single tab-delimited text file includes matrix raw count values of all samples (sample name in column and gene name in row).
Supplementary files format and content: a single tab-delimited text file includes matrix TPM values of all samples (sample name in column and gene name in row).
|
| |
|
| Submission date |
Aug 25, 2023 |
| Last update date |
Sep 20, 2023 |
| Contact name |
Mamy Jean de Dieu ANDRIANTERANAGNA |
| E-mail(s) |
mamy-jean-de-dieu.andrianteranagna@curie.fr
|
| Phone |
+33156246274
|
| Organization name |
Institut Curie
|
| Department |
Centre de Recherche
|
| Lab |
U900
|
| Street address |
26 rue d'Ulm
|
| City |
Paris |
| State/province |
Ile de France |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE241734 |
Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups [bulkRNAseq_mouseRT_R26] |
| GSE242090 |
Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups |
|
| Relations |
| BioSample |
SAMN37182700 |
| SRA |
SRX21500338 |
