|
| Status |
Public on Jun 30, 2014 |
| Title |
Primary Tumor |
| Sample type |
RNA |
| |
|
| Source name |
primary lesion
|
| Organism |
Homo sapiens |
| Characteristics |
age: 58y
gender: male
tissue: oral squamous cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)
|
| Label |
Cy3
|
| Label protocol |
cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).
|
| |
|
| Hybridization protocol |
cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8×60K ; Agilent Technologies) according to the manufacturer's instructions.
|
| Scan protocol |
The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.
|
| |
|
| Submission date |
Feb 04, 2014 |
| Last update date |
Jun 30, 2014 |
| Contact name |
Takahiro Fujinaga |
| E-mail(s) |
takahiro@dent.kyushu-u.ac.jp
|
| Organization name |
Kyushu University
|
| Department |
Faculty of Dental Science
|
| Lab |
Division of Maxillofacial Diagnostic and Surgical Sciences
|
| Street address |
3-1-1 Maidashi Higashi-ku
|
| City |
Fukuoka |
| State/province |
Fukuoka |
| ZIP/Postal code |
812-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE54672 |
Analysis of biological characterization and metastasis-related genes in cell lines derived from the Primary lesion and lymph node metastasis of a squamous cell carcinoma arising in the mandibular gingiva |
|
