|
| Status |
Public on Apr 28, 2024 |
| Title |
RNA-seq, PIC496-3 in vitro, AG120+IFNg, Replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
cell line: PIC496-3
cell type: glioma
genotype: Cas9; Pik3ca-H1047R; Idh1-R132H; Trp53KO; AtrxKO
treatment: AG120 + IFNgamma
|
| Treatment protocol |
This study used the mIDH inhibitor, AG120 (Servier Pharmaceuticals). Murine glioma (PIC496-3) spheroid cells were treated for five days with either DMSO or 1 μM mIDH inhibitor (AG120). Where indicated, 10ng/mL IFNγ was added for the final two days of culturing. Cells were collected for RNAseq on the fifth day.
|
| Growth protocol |
Murine glioma spheroid 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).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell suspensions from cells cultured in a monolayer were homogenized in 300 to 600 μL of TRIzol. RNA was extracted from homogenized samples using the Direct-zol RNA Miniprep Plus Kit in accordance with the manufacturer’s suggested protocol.
The library was constructed by rRNA depletion by Ribo-ZeroTM & NEB directional library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNAseq_PIC496_AI3
|
| Data processing |
Adapter sequences were trimmed using Trimmomatic (v0.36)
Pre- and post- trimming quality control was done using FastQC (v0.11.7).
For protein coding gene transcripts, trimmed reads were quantified by pseudoalignment to mm10 using Kallisto (v0.46.0)
Protein coding gene counts were aggregated using the tximport (v1.24.0) R package
For transposable elements, trimmed reads were mapped to mm10 and quantified using SQuIRE (v0.9.9.9a)
Assembly: mm10
Supplementary files format and content: comma-separated text file includes raw counts for protein coding genes in each sample
Supplementary files format and content: comma-separated text file includes raw counts for transposable elements in each sample
|
| |
|
| Submission date |
Apr 23, 2024 |
| Last update date |
Apr 28, 2024 |
| Contact name |
Robert Manguso |
| E-mail(s) |
rmanguso@broadinstitute.org
|
| Organization name |
Broad Institute of MIT and Harvard
|
| Street address |
75 Ames Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE264725 |
Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity [mouse_glioma_rnaseq] |
| GSE264730 |
Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity |
|
| Relations |
| BioSample |
SAMN41065068 |
| SRA |
SRX24349907 |
