|
| Status |
Public on Apr 24, 2024 |
| Title |
GEMM derived GSC line PIC496-3 bio rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
cell line: PIC496-3
cell type: glioma stem-like cells
genotype: IDH1 mutant
|
| Treatment protocol |
NA
|
| Growth protocol |
Murine GSC cells were cultured in NeuroCult NS-A Basal Medium (Mouse) with Proliferation Supplement (StemCell Technologies 05701) supplemented with EGF (20 ng/mL), bFGF (20 ng/mL), heparin (2 μg/mL), 1% penicillin/streptomycin, amphotericin B (250 ng/mL), and Plasmocin (2.5 μg/mL). All murine GSC lines were cultured on ultra-low adherence plates (Corning 4615) in the presence of 5% CO2 and 5% oxygen at 37°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from fresh cell pellets using the RNeasy Blood & Tissue Kit (Qiagen) following the manufacturer’s instructions.
mRNA sequencing of mouse GSC lines was performed by Novogene. Brifly, total RNA served as input for polyA-RNA capture and rRNA removal. Strand-specific libraries were prepared and paired-end 150 bp sequencing was performed using an Illumina NovaSeq 6000 machine.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
PIC4963_rep2
|
| Data processing |
The sequencing reads were filtered to remove adapter contamination and low quality reads and processed reads were aligned by HiSat2 mouse (UCSC mm39) references for quantification.
Assembly: UCSC mm39
Supplementary files format and content: tab-delimited text file including FPKM values for each sample
|
| |
|
| Submission date |
Apr 24, 2024 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Samuel McBrayer |
| E-mail(s) |
samuel.mcbrayer@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Children's Research Institute
|
| Lab |
McBrayer Lab
|
| Street address |
6000 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390-8502 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE265829 |
Mutant IDH1 inhibition activates tumor immunity via endogenous reverse transcriptase and dsDNA sensing |
|
| Relations |
| BioSample |
SAMN41074640 |
| SRA |
SRX24360813 |
