|
| Status |
Public on Sep 20, 2023 |
| Title |
primary ATRT, ATRT01 |
| Sample type |
SRA |
| |
|
| Source name |
primary ATRT
|
| Organism |
Homo sapiens |
| Characteristics |
anatomic location: Cerebral Cortex
age at_diagnosis: 2
genotype: SMARCB1-mutated
tissue: primary ATRT
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was obtained from 10 fresh-frozen tumour samples using the Qiagen RNAeasy kit (Qiagen, Venlo, Netherlands), according to the manufacturer’s procedure.
Barcode Illumina compatible libraries were generated from 750 ng of total RNA for each sample using the TruSeq Stranded mRNA Library Preparation Kit (Illumina). Libraries were sequenced using the Illumina HiSeq 2500 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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 GRCh39/hg19 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: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: a single tab-delimited text file include TPM values for each Sample
|
| |
|
| Submission date |
Aug 29, 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 |
GPL24676 |
| Series (2) |
| GSE241831 |
Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups [bulkRNAseq_primaryATRT] |
| GSE242090 |
Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups |
|
| Relations |
| BioSample |
SAMN37185600 |
| SRA |
SRX21502486 |
