|
| Status |
Public on Jan 20, 2012 |
| Title |
gastric cancer case1-LN |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
gastric cancer : FFPE sample
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
case: 1
the depth of invasion: submucosal
the portion of lcm: metastatic lymph node
lymph node metastasis: +
|
| 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 |
non-neoplestic gastric mucosa : FFPE sample
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
case: 1
the depth of invasion: submucosal
the portion of lcm: metastatic lymph node
lymph node metastasis: +
|
| 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 24 h
|
| Scan protocol |
A microarray was scanned using Microarray acanner (Agilrny Technologies) at a pixel resolution size of 5?m
|
| Description |
Non-neoplastic tissue in the same patient was 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 |
Jan 21, 2011 |
| Last update date |
Jan 20, 2012 |
| Contact name |
Yoshiyuki Tsukamoto |
| E-mail(s) |
tuka@oita-u.ac.jp
|
| Organization name |
Oita university, Faculty of Medicine
|
| Department |
Molecular Pathology
|
| Street address |
hasamacho idaigaoka 1-1
|
| City |
Yufu-city |
| State/province |
Oita |
| ZIP/Postal code |
879-5593 |
| Country |
Japan |
| |
|
| Platform ID |
GPL8841 |
| Series (1) |
| GSE26800 |
Intratumoral genomic heterogeneity in submucosal-invasive gastric cancer |
|
