|
| Status |
Public on Feb 07, 2017 |
| Title |
SK-N-DZ SNP Array |
| Sample type |
genomic |
| |
|
| Source name |
neuroblastoma-derived cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SK-N-DZ
cell type: neuroblastoma-derived cell line
growth media: RPMI 1640, 10% FBS, 1% Penicillin/Streptomycin, 2mM L-Glutamine
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using Qiagen Dneasy blood & tissue kit
|
| Label |
Cy3, Cy5
|
| Label protocol |
Labeled single-bases (corresponding to the locus of interest) are extended from the oligos bound to the beads. C and G nucleotides are biotin-labeled and A and T nucleotides are dinitrophenyl labeled. The BeadChip then undergoes a series of staining steps to enable the beads to fluoresce and is washed and coated for imaging.
|
| |
|
| Hybridization protocol |
The resuspended DNA is heat-denatured and dispensed onto the BeadChip. The DNA migrates under the gasket by capillary action and spreads over one entire region of the BeadChip. Overnight, the DNA fragments anneal to their locus-specific 50-mer oligos, which are covalently linked to the beads. Each bead represents one locus, though there are at least 20 replicates of each bead-type per sample.
The unhybridized and non-specifically hybridized DNA is washed away with buffer and prepared for the X-Stain process.
|
| Scan protocol |
The BeadChips are then scanned by an Illumina iScan or BeadArray Reader. A laser is used to excite the flurophores of the labeled and extended bases. The scanner software then captures high-resolution images of the beads and saves the data onto the server.
|
| Data processing |
IDATS were imported into Illumina's Genome Studio, along with pertinent manifest and cluster files for array version humanomniexpress-24v1-0_a to generate various SNP values, and visualize in genome studio to detect breakpoints (*processed.txt).
|
| |
|
| Submission date |
Nov 17, 2016 |
| Last update date |
Sep 25, 2019 |
| Contact name |
Jo Lynne Rokita |
| E-mail(s) |
rokita@email.chop.edu
|
| Organization name |
Children's Hospital of Philadelphia
|
| Street address |
3501 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21168 |
| Series (2) |
| GSE89968 |
Genome-wide SNP Profiling of 27 Neuroblastoma Cell Lines |
| GSE89969 |
Genomic Profiling of Neuroblastoma Cell Lines |
|
