|
| Status |
Public on Jan 01, 2019 |
| Title |
primary melanocyte C15_1 |
| Sample type |
genomic |
| |
|
| Source name |
primary melanocyte
|
| Organism |
Homo sapiens |
| Characteristics |
disease: Melanocyte
tissue: SKin
|
| Growth protocol |
Primary melanocyte cultures were grown in Dermal Cell Basal Medium (ATCC® PCS-200-030™) supplemented with Melanocyte Growth Kit (ATCC® PCS-200-041™) and 1% Amphotericin B/Penicillin/Streptomycin (120-096-711, Quality Biological) at 37°C with 5% CO2, and trypsinized with Trypsin/EDTA Solution (R-001-100, Cascade Biologics) as well as Trypsin Neutralizer Solution (R-002-100, Cascade Biologics). Media was changed every 2-3 days when necessary.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from primary melanocyte cultrue using Gentra Puregene Cell Kit (158745, Qiagen)
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
200ng of genomic DNA, quantitated using Quant-iT™ PicoGreen dsDNA Reagent (ThermoFisher Scientific, Waltham, MA, USA) is denatured and neutralized, then isothermally amplified by whole-genome amplification. The amplified product is enzymatically fragmented, then precipitated and re-suspended.
|
| |
|
| Hybridization protocol |
Resuspended samples are denatured, then hybridized to locus-specific 50-mer oligonucleotides which are attached to 1-micron beads on the BeadChip. These 50-mer probes stop one base before the location of interest. Enzymatic single-base extension of the oligos on the BeadChip, using the captured DNA as a template, incorporates tagged nucleotides on the BeadChip, which are subsequently fluorophore-labeled during staining. The fluorescent label determines the genotype call for the sample.
|
| Scan protocol |
The Illumina iScan scans the BeadChips at two wavelengths to detect the fluorescent label, creating image files that are converted into genotype calls based on the detected fluorescence.
|
| Description |
Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-24-v1-1_a Genotyping BeadChips (Illumina)
|
| Data processing |
Genomic DNA extracted from primary melanocytes was genotyped using Illumina Infinium human OmniExpress array
|
| |
|
| Submission date |
Jul 21, 2017 |
| Last update date |
Jan 01, 2019 |
| Contact name |
Kevin M Brown |
| Organization name |
National Cancer Institute
|
| Department |
Division of Cancer Epidemiology & Genetics
|
| Lab |
Laboratory of Translational Genomics
|
| Street address |
8717 Grovemont Circle
|
| City |
Gaithersburg |
| State/province |
MD |
| ZIP/Postal code |
20877 |
| Country |
USA |
| |
|
| Platform ID |
GPL22678 |
| Series (2) |
| GSE101771 |
Expression quantitative trait loci of primary melanocytes facilitate identification of melanoma susceptibility genes |
| GSE166102 |
Cell-type specific multi-QTL analyses of cultured human primary melanocytes |
|
