|
| Status |
Public on Apr 30, 2024 |
| Title |
RNA-seq, total RNA, 2205 in vivo, sgCtrl, 3-day AG120, Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
cholangiocarcinoma
|
| Organism |
Mus musculus |
| Characteristics |
tissue: cholangiocarcinoma
cell line: 2205
cell type: tumor cells
genotype: Albumin-Cre; KrasG12D; IDH1R132C
treatment: AG120
|
| Treatment protocol |
Tumor-bearing mice were treated (~100 mm^3 starting volume) with vehicle or AG120 (150 mg/kg; twice daily)
|
| Growth protocol |
Immunocompetent mice harboring subcutaneous allograft tumors generated with murine CKIR132C ICC cells (2205-sgCtrl, -sgTet2) .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were harvested at serial time points (Vehcle, AG120-Day3 and AG120-Day 6). sgCtrl, sgTet2 CKIR132C ICC cells were isolated by magnetic bead–mediated depletion of stromal populations from tumors treated with vehicle or AG120 for 3 or 6 days. 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 |
| |
|
| 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 29, 2024 |
| Last update date |
Apr 30, 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) |
| GSE264730 |
Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity |
| GSE266170 |
Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity [mouse_vivo_tet2_rnaseq] |
|
| Relations |
| BioSample |
SAMN41127364 |
| SRA |
SRX24402612 |
