|
| Status |
Public on Apr 28, 2024 |
| Title |
WGBS, SNU1079 in vitro, DMSO, Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
cholangiocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cholangiocarcinoma
cell line: SNU1079
cell type: tumor cells
genotype: Known: IDH1R132C; CDKN2A.del; PBRM1.fs
treatment: DMSO
|
| Treatment protocol |
This study used the mIDH inhibitor, AG120 (Servier Pharmaceuticals). Human ICC (SNU1079) 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.
|
| Growth protocol |
Human IDH1R132C ICC cell line (SNU1079) were cultured in RPMI 1640 (+) L-glutamine, 25 mmol/L HEPES containing 10% FBS and 1% penicillin–streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNAs from single-cell suspensions from cells cultured in a monolayer were extracted from homogenized samples using the QIAamp DNA Mini Kit in accordance with the manufacturer’s suggested protocol.
EZ DNA Methylation Gold Kit (Zymo Research) for DNA bisulfite conversion and Accel-NGS® Methyl-Seq DNA Library Kit for lib prep
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| 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).
Bismark (v0.24.0, Babraham Bioinformatics, wrapper around Bowtie2) was used to align reads to the hg38 genomes with default parameters.
The Bismark function deduplicate_bismark was used to remove read duplicates from alignment files.
The bismark_methylation_extractor function was used to quantify methylated sites with the parameters “-p --comprehensive --no_overlap –bedgraph”.
Assembly: hg38
Supplementary files format and content: COV files outputted by bismark which has percent methylation and methylated and total read counts for each CpG
|
| |
|
| Submission date |
Apr 25, 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 |
GPL24676 |
| Series (2) |
| GSE264730 |
Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity |
| GSE265854 |
Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity [human WGBS] |
|
| Relations |
| BioSample |
SAMN41085517 |
| SRA |
SRX24373101 |
