|
| Status |
Public on Dec 08, 2023 |
| Title |
MCviPI_1 |
| Sample type |
genomic |
| |
|
| Source name |
HepG2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: MCviPI overexpressing
cel type: HepG2
treatment: none
replicate: biological replicate 1
|
| Treatment protocol |
24h treatment with 1mM FFA (Oleic acid and palmitic acid in a 2:1 ratio)
|
| Growth protocol |
The Human hepatoma cells (HepG2) cell lines overexpressing mitochondria targeted DNMTs MCviPI or inactivated MCviPI (MCviPI mutant) were cultured in Dulbecco’s modified Eagle medium (DMEM, Gibco, Thermo Fisher Scientific, 41965039) supplemented with 10% foetal bovine serum (Gibco, Thermo Fisher Scientific, 10270106), 1% penicillin-streptomycin solution (Gibco, Thermo Fisher Scientific, 15140122) and 1mM pyruvate. Both cell lines were cultured in T75 or T25 flasks in a humidified atmosphere (37°C and 5% CO2).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted and purified from fresh cell pellets using Qiagen DNeasy Kit according to standard instructions
|
| Label |
Cy3, Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC array using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting
|
| Data processing |
Raw intensity data from IDAT files was read and processed in R (v. 4.2.0) via the minfi R package. Data pre-processing consisted of masking probes with poor design, control probes, X-/Y chromosome probes and non-cg and non-ch probes. For quality control, the ratio of log2 median intensities (methylated and unmethylated) along with β-value densities, were calculated. β-values were then further processed using ChAMP (v 2.21.1). The difference in signal intensity between the two-colour channels (dye bias correction) was corrected for using the beta mixture interquartile matrix (BMIQ) method.
|
| |
|
| Submission date |
Aug 16, 2023 |
| Last update date |
Dec 08, 2023 |
| Contact name |
Claudia Theys |
| E-mail(s) |
claudia.theys@uantwerpen.be
|
| Organization name |
Universiteit Antwerpen
|
| Department |
FBD
|
| Lab |
PPES
|
| Street address |
Universiteitsplein,1
|
| City |
Wilrijk |
| State/province |
Antwerpen (nl) |
| ZIP/Postal code |
2610 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE240988 |
Mitochondrial GpC and CpG DNA hypermethylation cause metabolic stress induced mitophagy and cholestophagy |
|
