|
| Status |
Public on Jun 17, 2024 |
| Title |
Skin_congenital_melanocytic_nevus_patient_CMN16 |
| Sample type |
genomic |
| |
|
| Source name |
Skin
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Skin
cell type: Melanocyte, keratinocyte, fibroblast cells, others
genotype: NRAS Q61R
treatment: None
|
| Treatment protocol |
None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from flash-frozen biopsies or paraffin blocks using standard salting-out techniques.
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Bisulfite treatment was carried out to convert 500 ng of DNA into unmethylated cytosine nucleotides to uracil using the EpiJET Bisulfite Conversion Kit (ThermoFisher Scientific).
|
| |
|
| Hybridization protocol |
DNAs were hybridized to an Infinium Methylation EPIC v1 BeadChip arrays (Illumina)
|
| Scan protocol |
Scanned using an Illumina iSCAN platform.
|
| Data processing |
Preprocessing and quality control of the sample intensity data (IDAT) files were performed using the R package Minfi package (v.1.48.0). Sample normalization was done with the preprocessQuantile function. Once our data was combined with publicly available datasets (GSE188593), cell-type deconvolution was performed using the Epidish function, and using a reference library for DNA methylation-based cell-type deconvolution containing melanocyte, keratinocyte, and fibroblast cells. After filtering, normalization, and deconvolution differentially methylated probes were identified through mixed linear regression models using a Limma package from R.
|
| |
|
| Submission date |
May 31, 2024 |
| Last update date |
Oct 02, 2024 |
| Contact name |
Daniel Aldea |
| E-mail(s) |
daniel.ALDEA-ARIAS@univ-amu.fr
|
| Organization name |
Aix-Marseille University
|
| Street address |
27 Bd Jean Moulin
|
| City |
Marseille |
| ZIP/Postal code |
13385 |
| Country |
France |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE268769 |
Deconvoluted methylation profiles discriminate between closely related melanocytic nevi |
|
