|
| Status |
Public on Jan 31, 2015 |
| Title |
Case_3_father |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
whole blood sample
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
tissue: whole blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from whole blood using Qiagen genomic DNA extraction kit following manufacturer's specifications
|
| Label |
Cy5
|
| Label protocol |
1 microgram DNA was labeled with Cy5 (case) or Cy3 (controls) using Exo-Klenow enzyme according to the manufacturer's specifications (Agilent Array-Based CGH for Genomic DNA Analysis version 4.0, June 2006).
|
| |
|
| Channel 2 |
| Source name |
whole blood from 100 male controls
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: pool of DNA from whole blood samples of 100 male controls
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from whole blood using Qiagen genomic DNA extraction kit following manufacturer's specifications
|
| Label |
Cy3
|
| Label protocol |
1 microgram DNA was labeled with Cy5 (case) or Cy3 (controls) using Exo-Klenow enzyme according to the manufacturer's specifications (Agilent Array-Based CGH for Genomic DNA Analysis version 4.0, June 2006).
|
| |
|
| |
| Hybridization protocol |
Labeled DNA was mixed with Hybridization buffer, Blocking Agent and Cot-1 DNA and heated for 3 minutes at 95 C followed by incubation at 37 C for 30 minutes. Hybridization was carried out in Agilent SureHyb chambers using microarray slides and gasket slides for 40 hours at 65 C followed by sequential washes according to the manufacturer's protocol.
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
|
| Description |
profiling of germline copy number variations
Father3
|
| Data processing |
Data processing was performed using Feature Extraction and DNA analytics software (Agilent)
|
| |
|
| Submission date |
Jan 30, 2015 |
| Last update date |
Jan 31, 2015 |
| Contact name |
Wigard Kloosterman |
| E-mail(s) |
w.kloosterman@umcutrecht.nl
|
| Organization name |
University Medical Center Utrecht
|
| Street address |
Universiteitsweg 100
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CG |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL8693 |
| Series (2) |
| GSE65453 |
Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring [case 3] |
| GSE65454 |
Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring. |
|
