|
Status |
Public on Feb 20, 2007 |
Title |
87 |
Sample type |
genomic |
|
|
Source name |
blood or lymphoblast
|
Organism |
Homo sapiens |
Characteristics |
familyID=8254-101;gender=F;status=unaffected;relation=mother
|
Extracted molecule |
genomic DNA |
Extraction protocol |
standard phenol/chloroform method
|
Label |
Biotin Streptavidin Phycoerythin (SAPE)
|
Label protocol |
See Affymetrix GeneChip Mapping 10K 2.0 Assay Manual, experiments were run in 96-well plate format 1. Prepare Labeling Mix as master mix ON ICE and vortex at medium speed for 2 seconds (for multiple samples, make 5% excess). 2. Aliquot 19.4 uL of Labeling Master Mix into the fragmentation plate containing 50.6 uL of fragmented DNA samples. 3. Seal the plate tightly with a plate cover. 4. Vortex the plate at medium speed for 2 seconds, and briefly spin the plate at 2,000 rpm for 1 minute. 5. Run the following program: 37ºC for 2 hours, 95ºC for 15 minutes, 4ºC Hold. 6. Briefly spin the plate at 2,000 rpm for 1 minute after the labeling reaction.
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|
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Hybridization protocol |
See Affymetrix GeneChip Mapping 10K 2.0 Assay. 1. Prepare the Hybridization Cocktail Master Mix (for multiple samples make 5% excess). 2. Transfer each of the labeled sample from the plate to a 1.5 mL Eppendorf tube. Aliquot 190 uL of the Hybridization Cocktail Master Mix into the 70 uL of labeled DNA samples. 3. Heat the 260 uL of hybridization mix and labeled DNA at 95°C in a heat block for 10 minutes to denature. 4. Cool down on crushed ice for 10 seconds. 5. Spin briefly at 2,000 rpm for 1 minute in a microfuge to collect any condensate. 6. Place the tubes at 48°C for 2 minutes. 7. Inject 80 uL denatured hybridization mix into the array. 8. Hybridize at 48°C for 16 to 18 hours at 60 rpm.
|
Scan protocol |
See Affymetrix GeneChip Mapping 10K 2.0 Assay Manual. Fluidics Station 450/250 was used to automate the washing and staining of GeneChip® Mapping probe arrays. Arrays were scanned with the GeneChip® Scanner 3000 using GeneChip Operating Software (GCOS)
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Description |
NAAR010-C6-8258-204
|
Data processing |
Genotype calls were made using Affymetrix GeneChip Operating Software (GCOS) and Affymetrix GeneChip DNA Analysis Software (GDAS). Copy number variation was inferred using DNA Chip Analyzer (dCHIP).
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|
|
Submission date |
Feb 18, 2007 |
Last update date |
Feb 21, 2007 |
Contact name |
Christian R. Marshall |
URL |
http://www.tcag.ca/
|
Organization name |
The Hospital for Sick Children
|
Department |
Genetics & Genome Biology
|
Street address |
101 College St.
|
City |
Toronto |
State/province |
ON |
ZIP/Postal code |
M5G 1L7 |
Country |
Canada |
|
|
Platform ID |
GPL2641 |
Series (1) |
GSE6754 |
Mapping autism risk loci using genetic linkage and chromosomal rearrangements |
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