|
Status |
Public on Apr 24, 2024 |
Title |
GEMM derived GSC line PIC144-3 bio rep 3 |
Sample type |
SRA |
|
|
Source name |
brain
|
Organism |
Mus musculus |
Characteristics |
tissue: brain cell line: PIC144-3 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 |
PIC1443_rep3
|
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 |
SAMN41074642 |
SRA |
SRX24360811 |