|
| Status |
Public on Jul 12, 2012 |
| Title |
ID patient 5 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
DNA patient 5
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lymfocytes
disease: intellectual disability/autism
gender: male
age: child
|
| Treatment protocol |
none
|
| Growth protocol |
not applicable
|
| 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 |
Cy3
|
| Label protocol |
As per manufacturer (Agilent)
|
| |
|
| Channel 2 |
| Source name |
sex matched DNA control pool of at least 10 different healthy individuals
|
| Organism |
Homo sapiens |
| Characteristics |
reference: sex matched DNA control pool of at least 10 different healthy individuals
|
| Treatment protocol |
none
|
| Growth protocol |
not applicable
|
| 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 |
Cy5
|
| Label protocol |
As per manufacturer (Agilent)
|
| |
|
| |
| Hybridization protocol |
Following standard manufacturer's procedures
|
| Scan protocol |
Scanned on an Agilent scanner
|
| Description |
hybridized to array Agilent 105k
|
| Data processing |
Data analysis using Genomic Workbench Standard Edition 5.0.14, the Admin-2 algorithm was used for calculation of log2 ratio's and for CNV-calling a minimum of 3 probes for deletions and 5 probes for duplications was taken into account.
|
| |
|
| Submission date |
Apr 10, 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 |
GPL8693 |
| Series (2) |
| GSE37141 |
Oligo array for CNV calling AUTS2 project [Agilent] |
| GSE37657 |
AUTS2 project |
|
