|
| Status |
Public on Sep 25, 2010 |
| Title |
GM17850 (550K) |
| Sample type |
genomic |
| |
|
| Source name |
lymphoblastoid cell line GM17850
|
| Organism |
Homo sapiens |
| Characteristics |
ethnic group: HCA Han Chinese-American
cell line (coriell id): GM17850
wei id: Wei747
cell type: EBV-transformed lymphoblastoid cells
|
| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM17850
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purchased from the Coriell Cell Repository (Camden, NJ), which was extracted from the cell cultures in the Repositories
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
750 ng of high quality DNA samples are denatured and neutralized, and then are isothermally amplified in an overnight step. The amplified product is fragmented by a controlled enzymatic process that does not require gel electrophoresis. The process uses end-point fragmentation to avoid overfragmenting the sample. After an isopropanol precipitation, the fragmented DNA is collected by centrifugation at 4ºC, and resuspended in a hybridization buffer.
|
| |
|
| Hybridization protocol |
Samples are applied to each BeadChip. The loaded BeadChip is incubated overnight in the Illumina Hybridization Oven. The amplified and fragmented DNA samples anneal to locus-specific 50mers (covalently linked to one of over 500,000 bead types) during hybridization. One bead type corresponds to each allele per SNP locus. Unhybridized and non-specifically hybridized DNA is washed away. The chip undergoes staining and extension in capillary flow-through chambers. Singlebase extension of the oligos on the BeadChip, using the captured DNA as a template, incorporates detectable labels on the BeadChip and determines the genotype call for the sample.
|
| Scan protocol |
The Illumina BeadArray Reader scans the BeadChip, using a laser to excite the fluorophore of the single-base extension product on the beads. The scanner records high-resolution images of the light emitted from the fluorophores.
|
| Description |
Genomic DNA extracted from lymphoblastoid cell line was genotyped using Infinium HumanHap550-v3 Genotyping BeadChips (Illumina).
|
| Data processing |
Genomic DNA extracted from cultured lymphoblastoid cell lines was genotyped using HumanHap550 v3.0 Whole-Genome Genotyping Kit (Illumina).
|
| |
|
| Submission date |
Sep 21, 2010 |
| Last update date |
Sep 24, 2010 |
| Contact name |
Liewei Wang |
| E-mail(s) |
wang.liewei@mayo.edu
|
| Phone |
507-284-5264
|
| Fax |
507-284-4455
|
| URL |
http://mayoresearch.mayo.edu/staff/wang_l2.cfm
|
| Organization name |
Mayo Clinic
|
| Department |
Molecular Pharmacology and Experimental Therapeutics
|
| Street address |
200 First street SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL6434 |
| Series (2) |
| GSE24260 |
Genome-wide SNP array data from Human Variation Panel by Illumina 550K |
| GSE24277 |
Human Variation Panel: Gene Expression and Genotype |
|
