|
Status |
Public on Jan 01, 2019 |
Title |
primary melanocyte C134_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 |
|