|
| Status |
Public on Sep 23, 2016 |
| Title |
patient 07, metastatic lymph node, copy number status |
| Sample type |
genomic |
| |
|
| Source name |
metastatic lymph node of patient 07
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: oral tongue squamous cell carcinoma (OTSCC)
individual: patient 07
tissue: metastatic lymph node (MLN)
data_type: copy number
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
All samples were formalin-fixed paraffin-embedded (FFPE) tissues. Sections of 4 μm were cut from each FFPE tissue and mounted onto slides. After confirmation of the tumor area by pathological examination, the viable cancer cell populations were isolated from each slide-mounted section using scalpels. Dissected samples were collected for each sample and DNA extraction was performed using the QIAamp DNA FFPE Tissue Kit (QIAGEN) according to the manufacturer’s protocol. For each sample, genomic DNA was isolated, purified, and then eluted in ATE buffer, low EDTA, pH 8.3. The double-stranded genomic DNA was quantified using a Qubit 2.0 Fluorometer (Life Technologies) and diluted to 12 ng/μL.
|
| Label |
biotin
|
| Label protocol |
Genomic DNA (80 ng per each sample) was labeled by OncoScan FFPE Assay Kit (Affymetrix) according to manufacturer's instruction.
|
| |
|
| Hybridization protocol |
The products were digested using HaeIII, mixed with the hybridization cocktail, denatured, and hybridized to the GeneChip OncoScan Arrays (Affymetrix)
|
| Scan protocol |
The hybridized arrays were finally washed and stained in a GeneChip Fluidics Station (Affymetrix) and scanned using a GeneChip Scanner (Affymetrix).
|
| Description |
11-L10_A_(OncoScan).CEL
11-L10_C_(OncoScan).CEL
metastatic lymph node of patient 07
CN_07-L
|
| Data processing |
Genome-wide copy number and loss of heterozygosity data were included in the .CEL files. The two files for each allele were collated for analysis in the .OSCHP files, which were quality checked using OncoScan Console Software (Affymetrix). Genome-wide copy number and CN-LOH data were visualized using Nexus Express for OncoScan Software (ver.3 BioDiscovery) and the Tuscan algorithm. For statistical analysis, the status of copy number and LOH for each patient was calculated by Chromosome Analysis Suite (Affymetrix), and the obtained data in text file format was further analyzed by R statistical software (http://www.r-project.org/).
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| |
|
| Submission date |
Dec 15, 2015 |
| Last update date |
Sep 23, 2016 |
| Contact name |
Takuma Morita |
| E-mail(s) |
morimfs@tmd.ac.jp
|
| Phone |
+81-3-5803-5500
|
| Organization name |
Tokyo Medical and Dental University
|
| Department |
Maxillofacial Surgery
|
| Street address |
1-5-45 Yushima, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-8549 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18602 |
| Series (1) |
| GSE76014 |
Characterizing genetic transitions of copy number alterations and allelic imbalances in metastatic process of the oral tongue carcinoma |
|
| Relations |
| Reanalyzed by |
GSM1972488 |
