|
Status |
Public on Oct 17, 2014 |
Title |
Human Male with Syndromic Intellectual disability_2_CGH-array |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
Peripheral blood DNA
|
Organism |
Homo sapiens |
Characteristics |
gender: male 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
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|
|
Channel 2 |
Source name |
pooled peripheral blood DNA from 11 healthy males
|
Organism |
Homo sapiens |
Characteristics |
gender: male 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.
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|
|
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 |
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