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Sample GSM8229751 Query DataSets for GSM8229751
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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