|
| Status |
Public on Oct 17, 2014 |
| Title |
Human Female with Syndromic Intellectual disability_1_CGH-array |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Peripheral blood DNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
sample type: test
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extraction was performed with a commercial kit QIAamp ® DNA Mini Kit (QIAGEN). The extraction was performed automatically, using equipment QIAcube (QIAGEN) with the recommended protocol with minor modifications.
|
| Label |
Cy3
|
| Label protocol |
test and control samples were first fragmented by enzymatic digestion and then were each labeled with a different fluorochrome, Cy5 (red) and Cy3 (green). 2000ng of DNA from both sample and reference were labeled with the Agilent Genomic DNA Labeling Kit PLUS
|
| |
|
| Channel 2 |
| Source name |
pooled peripheral blood DNA from 11 healthy females
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
sample type: reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extraction was performed with a commercial kit QIAamp ® DNA Mini Kit (QIAGEN). The extraction was performed automatically, using equipment QIAcube (QIAGEN) with the recommended protocol with minor modifications.
|
| Label |
Cy5
|
| Label protocol |
test and control samples were first fragmented by enzymatic digestion and then were each labeled with a different fluorochrome, Cy5 (red) and Cy3 (green). 2000ng of DNA from both sample and reference were labeled with the Agilent Genomic DNA Labeling Kit PLUS
|
| |
|
| |
| Hybridization protocol |
Hybridization protocol was the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol Version 4.0.
|
| Scan protocol |
Scanning was made with Agilent G2565BA. For feature extraction we used the Agilent Feature Extraction Software 9.5.31. The extraction protocol and metrics were the Agilent protocol CGH-v4_95_Feb07 and the QC Metric Set CGH_QCM_Feb07.
|
| Data processing |
The algorithm used are the Z-score and/or ADM-2. The supplementary files containing the normalized log2 ratios are available on the sample records. These files contain normalized log2 ratio representing test/reference.
|
| |
|
| Submission date |
Oct 16, 2014 |
| Last update date |
Oct 17, 2014 |
| Contact name |
Francisco Martinez |
| E-mail(s) |
martinez_fracas@gva.es
|
| Organization name |
Hospital Universitari i Politecnic La Fe
|
| Department |
Unidad de Genetica
|
| Street address |
Avenida Campanar 21
|
| City |
Valencia |
| State/province |
Valencia |
| ZIP/Postal code |
46009 |
| Country |
Spain |
| |
|
| Platform ID |
GPL8841 |
| Series (2) |
| GSE62439 |
Application of CGH-array for the detection of genomic rearrangements responsible for sindromic mental retardation of unknown cause |
| GSE62440 |
Application of CGH-array and SNP-array for the detection of genomic rearrangements responsible for sindromic mental retardation of unknown cause |
|
