|
| Status |
Public on Apr 02, 2012 |
| Title |
ESRD-RCC case9 atypical cyst |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ESRD-RCC : FFPE sample
|
| Organism |
Homo sapiens |
| Characteristics |
phenotype: atypical cyst
gender: Male
disease state: ESRD-RCC
tissue: RCC tumor
individual: case 9
|
| Treatment protocol |
standard proteinase K-digestion method
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Agilent Genomic DNA Labeling Kit Plus(Agilent)
|
| Label |
Cy5
|
| Label protocol |
dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65℃ for 24 h
|
| |
|
| Channel 2 |
| Source name |
control : FFPE sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: various non-neoplastic tissues from 12 patients
disease state: control
|
| Treatment protocol |
standard proteinase K-digestion method
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Agilent Genomic DNA Labeling Kit Plus(Agilent)
|
| Label |
Cy3
|
| Label protocol |
dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65℃ for 24 h
|
| |
|
| |
| Hybridization protocol |
A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5μm
|
| Scan protocol |
standard Agilent protocol
|
| Description |
Non-neoplastic tissues in the other 12 patients were used as the source of control DNA
|
| Data processing |
Microarray images were analyzed by using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were subsequently imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies).Microarray images were analyzed using FEATURE EXTRACTION v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_95_Feb07), and the resulting data were imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies). The log2ratio of Cy5 (tumor) to Cy3 (Control) was normalized by the Centralization Algorithm in DNA Analytics. Aberrant regions were determined by the ADM-2 algorithm at a threshold of 12.0 in DNA Analytics. To detect gains and losses, we set the values of parameters for aberration filters as: minimum number of probes in region 2, minimum absolute average log2ratio for region 0.263034, maximum number of aberrant regions 10000, and percentage penetrance per feature 0. We set the value of the minimum absolute average log2ratio at 0.263034 to detect regions showing a change in the averaged copy number equal to or more than 1.2-fold (log2(1.2)=0.263034).
|
| |
|
| Submission date |
Oct 20, 2011 |
| Last update date |
Apr 02, 2012 |
| Contact name |
Toru Inoue |
| E-mail(s) |
i-toru@med.oita-u.ac.jp
|
| Fax |
+81-97-586-5699
|
| Organization name |
Faculty of medicineOita University
|
| Department |
Department of Molecular Pathology
|
| Street address |
Hasama-machi 1-1
|
| City |
Yufu-City, Oita |
| ZIP/Postal code |
879-5593 |
| Country |
Japan |
| |
|
| Platform ID |
GPL8841 |
| Series (1) |
| GSE33117 |
Genomic profiling of 19 renal cell carcinoma samples from patients with end-stage renal disease |
|
