|
| Status |
Public on Apr 28, 2024 |
| Title |
RRBS, ICC21 in vitro |
| Sample type |
SRA |
| |
|
| Source name |
cholangiocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cholangiocarcinoma
cell line: ICC21
cell type: tumor cells
genotype: Known: IDH1 wildtype
treatment: N/A
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Human ICC cell lines included the patient-derived models established in Bardeesy lab and cholangiocarcinoma cell lines from other academic labs. The detail culture conditions are listed in the Materials and Methods section.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from frozen cell pellets using the DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer’s instructions and quantified using a NanoDrop.
RRBS libraries were prepared using the Ovation RRBS Methyl-Seq kit (Tecan Genomics, formerly Nugen Technologies) according to the v7 user guide following the True Methyl Module.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were assessed for QC with FastQC (Babraham Bioinformatics)
Reads were trimmed using Trim Galore (Babraham Bioinformatics, wrapper around Cutadapt for RRBS libraries), using the parameters “--paired -a AGATCGGAAGAGC -a2 AAATCAAAAAAAC.”
Diversity adapters were trimmed using the trimRRBSdiversityAdaptCustomers Python script available from Tecan Genomics.
Bismark aligner (Babraham Bioinformatics, wrapper around Bowtie2) was used to align sequencing reads to the hg38 human genome with default parameters.
The bismark_methylation_extractor function was used to quantify methylated sites with the parameters “-p --comprehensive –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 23, 2024 |
| Last update date |
Dec 10, 2024 |
| Contact name |
Robert T Manguso |
| E-mail(s) |
RMANGUSO@MGH.HARVARD.EDU, rmanguso@broadinstitute.org
|
| Phone |
5084980837
|
| Organization name |
Broad Institute of MIT & Harvard
|
| Street address |
75 Ames Street, Rm 7053
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE264722 |
Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity [RRBS] |
| GSE264730 |
Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity |
|
| Relations |
| BioSample |
SAMN41062700 |
| SRA |
SRX24348461 |
