|
| Status |
Public on Sep 20, 2023 |
| Title |
IC-032, DMSO, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
IC-032
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IC-032
cell type: ATRT cell lines
genotype: SMARCB1-mutated
treatment: DMSO
time: Day 7
|
| Treatment protocol |
3 independant samples of CHLA-02-ATRT and IC-032 cells were treated with DMSO or DAPT at 10 µM for 7 days.
|
| Growth protocol |
ATRT cell line CHLA-02-ATRT (#CRL-3020, ATCC) was cultured according to the manufacturer’s protocol. IC-032 cell line, established in Curie Institute from a supra-tentorial ATRT, was cultured in DMEM/F12 supplemented with 20 ng/mL FGF, 20 ng/mL EGF, and 1x B27 supplement (#15360284, Fisher Scientific).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted using the Nucleospin II kit (Macherey-Nagel). The tumor cell content was visually estimated before RNA extractions.
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 platforms in the 100 bp paired-end mode.
|
| |
|
| 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 genome were performed using STAR (version 2.5.3a) and the refFlat gene annotation downloaded from UCSC
duplicated reads were marked with picard and then 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 includes matrix of TPM values with sample in columns and genes on rows
|
| |
|
| 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 |
GPL24676 |
| Series (2) |
| GSE241733 |
Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups [bulkRNAseq_ATRT_cellLines] |
| GSE242090 |
Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups |
|
| Relations |
| BioSample |
SAMN37182661 |
| SRA |
SRX21500050 |
