|
| Status |
Public on Dec 13, 2022 |
| Title |
J_bis |
| Sample type |
SRA |
| |
|
| Source name |
WT+GCV
|
| Organism |
Mus musculus |
| Characteristics |
disease state: GBM
strain: 129/SVJ x C57BL/6 x FVB
genotype: GlastCreERT2/+; Ptenfl/fl
injected lentivirus: HRasV12-shp53-(IRES)-GFP-(2a)-Firefly-luciferase
|
| Treatment protocol |
GCV (25 mg/kg) was administered daily via i.p. injections for 5 consecutive days, starting when bioluminescence head/body ratio reached 2.
|
| Growth protocol |
The lentivirus (1 µL, 6 x 108 PFU/mL) was stereotaxically injected in the right SVZ of brain mice. From the next day, mice were injected i.p. with tamoxifen (TMX, 100 mg/kg) once per day for five consecutive days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from tumors were extracted following either via the Maxwell RSC simplyRNA Tissue (Promega, #AS1340) or the TRI-reagent (Molecular Center Research, #TR 118) procedures.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality of raw data was evaluated with FastQC.
Poor quality sequences were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on mm10 reference genome and quantification with gencode vM25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including expecting counts, TPM and FPKM
|
| |
|
| Submission date |
Mar 11, 2022 |
| Last update date |
Dec 13, 2022 |
| Contact name |
Isabelle Leroux |
| E-mail(s) |
isabelle.leroux@icm-institute.org
|
| Organization name |
Paris Brain Institute
|
| Street address |
47 Boulevard de l'Hôpital
|
| City |
Paris |
| ZIP/Postal code |
75013 |
| Country |
France |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE168040 |
Cellular senescence in malignant cells promotes tumorigenesis in mouse and patient glioblastoma. |
| GSE198439 |
Cellular senescence in malignant cells promotes tumorigenesis in mouse and patient glioblastoma [p16] |
|
| Relations |
| BioSample |
SAMN26582994 |
| SRA |
SRX14439263 |
