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Status |
Public on Sep 25, 2010 |
Title |
GM17107 (510S) |
Sample type |
genomic |
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Source name |
lymphoblastoid cell line GM17107
|
Organism |
Homo sapiens |
Characteristics |
ethnic group: AA African-American cell line (coriell id): GM17107 wei id: Wei023 cell type: EBV-transformed lymphoblastoid cells
|
Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM17107
|
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 4ÂșC, and resuspended in a hybridization buffer.
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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.
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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.
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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 Infinium HumanExon510S-2 DNA Analysis Kit (Illumina).
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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 |
GPL6988 |
Series (2) |
GSE24245 |
Genome-wide SNP array data from Human Variation Panel by Illumina 510S |
GSE24277 |
Human Variation Panel: Gene Expression and Genotype |
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