|
| Status |
Public on Jul 12, 2012 |
| Title |
ID patient 10 |
| Sample type |
genomic |
| |
|
| Source name |
DNA patient 10
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lymphocyte
disease: intellectual disability/autism
gender: female
age: toddler
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
|
| Label |
biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner
|
| Description |
hybridized to SNP array affymetrix 6.0
|
| Data processing |
The relative DNA copy numbers at the SNP/CNV loci from the Affymetrix platforms were determined by comparison of the normalised array signal intensity data for the proband’s DNA sample against the HapMap270 reference file provided by Affymetrix, using Genotyping Console or ChAS software (default settings). (see Laura Bernardini et. al., 2010)
|
| |
|
| Submission date |
Mar 30, 2012 |
| Last update date |
Jul 12, 2012 |
| Contact name |
Els Voorhoeve |
| E-mail(s) |
e.voorhoeve@vumc.nl
|
| Phone |
+31204440157
|
| Organization name |
VU medical center
|
| Department |
Clinical Genetics
|
| Lab |
Cytogenetics
|
| Street address |
De Boelelaan 1117
|
| City |
Amsterdam |
| ZIP/Postal code |
1081 HV |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE36950 |
SNP array for CNV calling AUTS2 project [Affymetrix] |
| GSE37657 |
AUTS2 project |
|
