|
| Status |
Public on Apr 28, 2024 |
| Title |
RNA-seq, SNU1079 in vitro, sgCGAS, AG120+IFNg, Replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
cholangiocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cholangiocarcinoma
cell line: SNU1079 sgCGAS
cell type: tumor cells
genotype: Known: IDH1R132C; CDKN2A.del; PBRM1.fs
treatment: AG120 + IFNγ
|
| Treatment protocol |
This study used the mIDH inhibitor, AG120 (Servier Pharmaceuticals). Human ICC cells (SNU1079 sgControl or sgcGAS) were treated for five days with either DMSO or 1 μM mIDH inhibitor (AG120) with or without Zidovudine/AZT. Where indicated, 10ng/mL IFNγ was added for the final two days of culturing.
|
| Growth protocol |
Human IDH1R132C ICC cell line (SNU1079 sgControl or sgcGAS) were cultured in RPMI 1640 (+) L-glutamine, 25 mmol/L HEPES containing 10% FBS and 1% penicillin–streptomycin.
|
| Extracted molecule |
polyA 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 NEB RNA Ultra™ II Directional kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
SNU1079_sgCGAS_AI3
|
| Data processing |
Raw sequencing reads were demultiplexed using bcl2fastq (v2.20.0)
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 hg38 using Kallisto (v0.46.0)
Protein coding gene counts were aggregated using the tximport (v1.24.0) R package
Assembly: hg38
Supplementary files format and content: comma-separated text file includes raw counts for protein coding genes in each sample
|
| |
|
| Submission date |
Apr 24, 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 |
GPL18573 |
| Series (2) |
| GSE264730 |
Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity |
| GSE265804 |
Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity [human_cgas_AZT_rnaseq] |
|
| Relations |
| BioSample |
SAMN41074489 |
| SRA |
SRX24360638 |
