|
| Status |
Public on Jul 11, 2012 |
| Title |
ACD lung_gDNA3 (sample 60.4) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Genomic DNA from frozen/FFPE lung tissue of ACD/MPV patient
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV)
tissue: lung
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Peripheral blood DNA was extracted using Gentra Puregene Blood Kit (Qiagen), DNA from frozen lung tissues was extracted using Dneast Blood & Tissue kit(Qiagen), DNA from FFPE lung tissues was isolated following manufacturer's protocol ( Agilent technologies)
|
| Label |
Cy3
|
| Label protocol |
0.5ug of genomic DNA was labeled using the NimbleGen Dual-color DNA labeling kit according to manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
Peripheral blood genomic DNA from normal control
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: healthy
tissue: peripheral blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Peripheral blood DNA was extracted using Gentra Puregene Blood Kit (Qiagen), DNA from frozen lung tissues was extracted using Dneast Blood & Tissue kit(Qiagen), DNA from FFPE lung tissues was isolated following manufacturer's protocol ( Agilent technologies)
|
| Label |
Cy5
|
| Label protocol |
0.5ug of genomic DNA was labeled using the NimbleGen Dual-color DNA labeling kit according to manufacturer's instructions.
|
| |
|
| |
| Hybridization protocol |
Labeled samples were hybridized to 4.2M whole genome arrays at 42°C for 60-72 hrs,followed by disassembling of slides from hybridization apparatus at 42° in the wash buffer containing DTT followed by three washes at room temperature in the same buffer for 2mins, 1min and 15secs respectively. The slides were dried in a microarray dryer for 1 min.
|
| Scan protocol |
4.2M microarrays were scanned on a Roche-NimbleGen MS 200 Microaarray scanner
|
| Data processing |
Scanned images were processed using NumbleScan v2.5 (Roche Nimblegen) and analyzed using Signalmap v1.9 (rocheNimbleGen)
|
| |
|
| Submission date |
Jul 11, 2012 |
| Last update date |
Jul 11, 2012 |
| Contact name |
Pawel Stankiewicz |
| E-mail(s) |
pawels@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Department |
Molecular Human Genetics
|
| Street address |
One Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL15746 |
| Series (2) |
| GSE39257 |
Genomic copy-number analysis in Alveolar capillary dysplasia (ACD) patient samples |
| GSE39258 |
Small non-coding differentially-methylated copy-number variants, involving lncRNAs, cause a lethal lung developmental disorder |
|
