|
| Status |
Public on May 03, 2024 |
| Title |
VDR, cell line, NC, biol rep1 |
| Sample type |
SRA |
| |
|
| Source name |
VDR cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: VDR cells
cell type: Medulloblastoma
|
| Treatment protocol |
Lentiviral infection with shRNAs. Cells were harvested 3 days after infection, the pellets were flash-frozen in liquid nitrogen and kept at -80°C until RNA extraction.
|
| Growth protocol |
Tumor cells for PDXs were isolated from PDX tumor chunks with a Percoll gradient. Both murine cell line and PDX cells were cultured and infected in adherent conditions (poly-D-lysine + matrigel precoated dishes). Growth medium for PDX and murine cells consisted of Neurobasal™ Medium (GIBCO) supplemented with 0.45% D+-Glucose (Sigma), 4 mM L-Glutamine (GIBCO), 100 U/mL penicillin/streptomycin (GIBCO), 1X Serum-free supplement B27 (GIBCO).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Plus Mini Kit (74134, Qiagen)
Stranded mRNA prep Ligation-Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNAseq v4.0 (Nextflow rna-seq analysis pipeline, Institute Curie)
raw sequencing reads checked for quality with Fastqc and trimmed for adapter sequences
Trimmed reads aligned on the human hg38 (PDXs) and mouse mm10 (VDR cells) reference genomes using the STAR mapper
Generation raw count table per gene and sample
Assembly: hg38 (PDXs KD NFI) / mm10 (VDR KD NFI)
Supplementary files format and content: tab-delimited text file includes raw counts for PDXs KD NFI dataset
Supplementary files format and content: tab-delimited text file includes raw counts for VDR KD NFI dataset
|
| |
|
| Submission date |
Aug 23, 2023 |
| Last update date |
May 03, 2024 |
| Contact name |
Jacob Torrejon Diaz |
| E-mail(s) |
jacob.torrejon-diaz@curie.fr
|
| Organization name |
Curie Institute
|
| Street address |
26 Rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE241602 |
Dynamic Chromatin Alteration Induces Oncogenic Hijacking by Nuclear Factor I Family Proteins for Medulloblastoma Progression |
|
| Relations |
| BioSample |
SAMN37129827 |
| SRA |
SRX21474110 |
