|
| Status |
Public on May 29, 2014 |
| Title |
atypical NF1 deletion patient_8 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
genomic DNA isolated from blood samples
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
tissue: blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was extracted from blood samples after cell lysis, proteinase treatment and purification of the DNA by ethanol precipitation.
|
| Label |
Cy5
|
| Label protocol |
Restriction enzymatic digestion of 0.5 µg genomic DNA from the patient as well as from a sex-matched control was performed with a mixture of AluI and RsaI at 37°C for two hours. Sample labelling of the restriction-digested genomic DNA samples with Cy5-dUTP or Cy3-dUTP, respectively, was performed using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies).
|
| |
|
| Channel 2 |
| Source name |
human genomic DNA, female (#1521, Promega)
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was extracted from blood samples after cell lysis, proteinase treatment and purification of the DNA by ethanol precipitation.
|
| Label |
Cy3
|
| Label protocol |
Restriction enzymatic digestion of 0.5 µg genomic DNA from the patient as well as from a sex-matched control was performed with a mixture of AluI and RsaI at 37°C for two hours. Sample labelling of the restriction-digested genomic DNA samples with Cy5-dUTP or Cy3-dUTP, respectively, was performed using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies).
|
| |
|
| |
| Hybridization protocol |
Sample hybridization and washing of the microarrays was carried out by means of the Oligo aCGH-on-chip Hybridization and Wash Buffer Kits (Agilent Technologies).
|
| Scan protocol |
Fluorescent intensities were detected with Scan Control A.8.4.1 Software on the Agilent DNA MicroarrayScanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies) and the design file 033151_D_F_20110323.xml.
|
| Data processing |
The software tools Feature Extraction 10.7.3.1 and Genomic Workbench Lite 6.0.130.24 (CGH module) were used for quality control by means of quality metrics, for annotation, statistical data analysis and visualization. The microarray data were normalized according to the following procedure: The expected average μ was subtracted from all log2 ratios vi. These modified log2 ratios vi are divided by the estimated variance σ. This transforms the log2 ratio scores into a normal distribution with a mean of 0 under the null model assumption. μ and σ were calculated from one or more microarrays according to the formula: vi → (vi - µ) / σ. The identification of aberrant regions was performed with the analysis software Genomic Workbench Lite using the aberration algorithm ADM-2 in combination with a centralization algorithm. The analysis of the microarrays was performed by IMGM Laboratories (Martinsried, Germany).
|
| |
|
| Submission date |
May 21, 2014 |
| Last update date |
May 29, 2014 |
| Contact name |
Julia Vogt |
| E-mail(s) |
ncbi@v-o-g-t.net
|
| Organization name |
Ulm University
|
| Department |
Institute of Human Genetics
|
| Street address |
Albert-Einstein Allee 11
|
| City |
Ulm |
| ZIP/Postal code |
89081 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18714 |
| Series (1) |
| GSE57859 |
SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints |
|
