|
| Status |
Public on Oct 16, 2014 |
| Title |
M2P |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
primary ccRCC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary ccRCC
age: 76
Sex: male
site: kidney
Stage: T1bN0M1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
standard proteinase K-digestion method
|
| Label |
Cy5
|
| Label protocol |
Agilent Genomic DNA Labeling Kit Plus(Agilent)
|
| |
|
| Channel 2 |
| Source name |
normal renal cortex
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: normal renal cortex
Sex: male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
standard proteinase K-digestion method
|
| Label |
Cy3
|
| Label protocol |
Agilent Genomic DNA Labeling Kit Plus(Agilent)
|
| |
|
| |
| Hybridization protocol |
dissolved in hybridization buffer (Agilent Oligo aCGH Hybridization Kit; Agilent Technologies), denatured and hybridized to the CGH array at 65C for 24 h
|
| Scan protocol |
A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5μm
|
| Description |
normal renal cortex obtained from each patient was used as the source of control DNA
|
| Data processing |
Microarray images were analyzed by using FEATURE EXTRACTION v.9.1.3.1, v.9.5.1.1 or v.9.5.3.1 (Agilent Technologies) with linear normalization (protocol CGH-v4_91 or CGH-v4_95_Feb07), and the resulting data were subsequently imported into the DNA Analytics v.4.0.81 software package (Agilent Technologies). Following normalization of the raw data, the log2ratio of Cy5 (tumor) to Cy3 (Control) was calculated. Aberrant regions were determined by the Aberration Detection Method-2 algorithm at a threshold of 6.0 in DNA Analytics. To detect gains and losses of chromosomal regions, we set the values of parameters for aberration filters as follows: minimum number of probes in region 2, minimum absolute average log2ratio for region 0.10, maximum number of aberrant regions 10000, and percentage penetrance per feature 0.
|
| |
|
| Submission date |
Jan 14, 2013 |
| Last update date |
Oct 17, 2014 |
| Contact name |
Takahiro Narimatsu |
| Organization name |
Oita University
|
| Department |
Medicine
|
| Lab |
Molecular Pathology
|
| Street address |
Hasamamachi Idaigaoka 1-1
|
| City |
Yufu |
| State/province |
Oita |
| ZIP/Postal code |
8795503 |
| Country |
Japan |
| |
|
| Platform ID |
GPL8841 |
| Series (1) |
| GSE43477 |
Genomic profiling of primary and metastatic clear cell renal cell carcinoma by array-based comparative genomic hybridization. |
|
