|
| Status |
Public on Jul 26, 2016 |
| Title |
Tumor tissue from patient 4 |
| Sample type |
RNA |
| |
|
| Source name |
OSCC tissue
|
| Organism |
Homo sapiens |
| Characteristics |
disease status: oral squamous cell carcinoma (OSCC)
Stage: T4N0M0
tissue: OSCC tissue
site: gingiva
Sex: male
age: 60
patient identifier: 4
|
| Treatment protocol |
Fresh OSCC tissues and normal oral mucosa were stored in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from tissues were extracted using TRIzol reagent following the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Arraystar Flash RNA Labeling Kit was used for sample labeling.
|
| |
|
| Hybridization protocol |
Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) was applied for hybridization as described by the manufacturer. Slides were hybridized at 65°C for 17h in Agilent's SureHyb Hybridization Chambers.
|
| Scan protocol |
After washing, slides were scanned with the Agilent DNA Microarray Scanner. Slides were assembled into scanner carousel, and then preceded one-color scanning procedure.
|
| Description |
240685T
|
| Data processing |
Data was extracted using Agilent Feature Extraction software. Results were provided in the Raw Data Files. Normalization was performed using the Agilent GeneSpring GX v12.0 software.
After quantile normalization of the raw data, lncRNAs that had at least 6 out of 12 samples with flags in Present or Marginal ("All Targets Value") were chosen for further data analysis. Differentially expressed lncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.
|
| |
|
| Submission date |
Jul 25, 2016 |
| Last update date |
Jul 26, 2016 |
| Contact name |
Guiquan Zhu |
| E-mail(s) |
gui_quanzhu@hotmail.com
|
| Organization name |
Sichuan Cancer Hospital
|
| Department |
Department of Head Neck Surgery
|
| Street address |
No.55 Section 4, Renmin South Road
|
| City |
Chengdu |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL16956 |
| Series (2) |
| GSE84805 |
Aberrant lncRNA expression profiles in OSCC tissues compared with paired normal oral mucosa |
| GSE84807 |
Long noncoding RNA HAS2-AS1 mediates hypoxia-induced invasiveness of oral squamous cell carcinoma |
|
