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Status |
Public on Jan 22, 2016 |
Title |
Invasive region of IPMN-inv (Case 30) |
Sample type |
genomic |
|
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Channel 1 |
Source name |
IPMN : FFPE sample
|
Organism |
Homo sapiens |
Characteristics |
gender: female
|
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 |
mixed genomic DNA of normal renal cortex : FFPE sample
|
Organism |
Homo sapiens |
Characteristics |
gender: 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 65℃ for 40 h
|
Scan protocol |
A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5μm
|
Description |
Genomic DNA was extracted from tissues of normal renal cortex obtained from 12 patients with ureteral or renal pelvic carcinoma, neither of which exhibited invasion or metastasis to the renal cortex. The same amount of genomic DNA extracted from 12 patients was mixed and used as the control DNA.
|
Data processing |
Microarray images were analyzed using FEATURE EXTRACTION v. 9.1 (Agilent Technologies) with linear normalization protocol CGH-v4_91 (Case 1-12) or CGH-v4_95_Feb07 (Case 14, 16-20, 22-31 and 40), and the resulting data were imported into DNA Analytics v. 3.4 (Agilent Technologies). After normalization of the raw data, the log2ratio of Cy5 (cancer) to Cy3 (control) was calculated. Next, aberrant regions were determined using the ADM-2 algorithm at a threshold of 8.0. To detect gains and losses, we set the values of parameters for the aberration filters as: minimum number of probes in region 2, minimum absolute average log2ratio for region 0.3, maximum number of aberrant regions 10,000, and percentage penetrance per feature 0. We set the value of the minimum absolute average log2 ratio at 0.3 to detect regions showing a change in the averaged copy number of more than 1.23-fold (log2(1.23) = 0.3).
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Submission date |
Jan 22, 2015 |
Last update date |
Jan 22, 2016 |
Contact name |
Naoki Hijiya |
E-mail(s) |
hijiya@oita-u.ac.jp
|
Phone |
1975865693
|
Organization name |
Oita University
|
Department |
Medicine
|
Lab |
Molecular pathology
|
Street address |
1-1, Idaigaoka Hasama-machi
|
City |
Yufu |
State/province |
Oita |
ZIP/Postal code |
879-5593 |
Country |
Japan |
|
|
Platform ID |
GPL9128 |
Series (1) |
GSE65181 |
Genomic profiling of IPMN with an associated invasive carcinomas (IPMN-inv) and invasive ductal carcinomas (IDC) by array-based comparative genomic hybridization |
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