|
| Status |
Public on Feb 20, 2020 |
| Title |
mGBM2-tumour-NT-5 |
| Sample type |
SRA |
| |
|
| Source name |
mouse glioblastoma tumour, of syngeneic transplant of glioblastoma cells generated in C57/Bl6N genetically engineered mouse model using double knock-out of Pten and Trp53
|
| Organism |
Mus musculus |
| Characteristics |
tissue: syngeneic mouse glioblastoma consisting of transplanted mGBM2 cells and host normal cells
|
| Treatment protocol |
Sox10 knockdown was carried out using lentivirus transduction of mGBM2 with the shSox10 (TRCN0000244290). All cells were Puromycin selected and Sox10 knockdown level was RT-PCR validated before injection. 200k cells (shNT and shSox10, in 1µl volume) were intracranially injected into adult C57/B6 mice (6 weeks age, female) brain under anesthesia with Isoflurane. Recipient mice were euthanised once severe symptoms became apparent.
|
| Growth protocol |
The primary mouse glioblastoma cell line (mGBM2) with Pten/Tp53 double knockout was established by the lab of Prof. Peter Angel in the German Cancer Research Center (DKFZ) (Costa et al. 2020, submitted). The cells used in these experiments are the result of two further in vivo passages of the cell line described previously (Costa et al., Blood Advances 2019). mGBM2 cells were characterized as the Proneural/RTK I subtype with high Sox10 expression based on RNA-seq profiling. mGBM2 cells were cultured at 37℃ in DMEM/F12 medium supplement with N2 supplement, EGF (20ng/ml), FGF (20ng/ml), Penicillin/Streptomycin and glutamine. The recipient C57/Bl6 mice were kept under standard conditions.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The tumour bulk was removed from the recipient animal, and cut into small pieces. Lysis was performed using the RLT buffer from, and total RNA was isolated using, the RNeasy kit (Qiagen) according to the manufacturer's protocol.
RNA-seq library preparation of each tumour (control, n=3; shSox10, n=5) was performed using the polyA-selected RNA-seq libraries preparation protocol with the TruSeq Stranded RNAseq Illumina kit by the DKFZ Genomics & Proteomics Core Facility. Libraries were multiplexed and sequenced in a single lane on a HiSeq 2000 v4, generating 50bp single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were aligned to the mouse genome (mm10 build) with the Gencode reference transcriptome (M2) using STAR (v2.3.0e).
Read counts for each gene were quantified as the total number of reads mapping to exons using featureCounts (Subread v1.5.3).
Gene expression values for each sample were quantified using the transcripts per million (TPM) metric.
Genome_build: mm10
|
| |
|
| Submission date |
Feb 19, 2020 |
| Last update date |
Feb 20, 2020 |
| Contact name |
Bernhard Radlwimmer |
| E-mail(s) |
b.radlwimmer@dkfz-heidelberg.de
|
| Organization name |
Deutsches Krebsforschungszentrum / German National Cancer Research Centre
|
| Department |
Department of Molecular Genetics
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE121723 |
Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype |
| GSE145556 |
Glioblastoma epigenome profiling identifies SOX10 as a master regulator of molecular tumour subtype - mouse RNAseq experiments |
|
| Relations |
| BioSample |
SAMN14137856 |
| SRA |
SRX7750542 |
