|
| Status |
Public on Jul 26, 2016 |
| Title |
Cal-27 cells cultured under hypoxia, replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
OSCC cell line, hypoxia
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Cal-27
cell type: oral squamous cell carcinoma (OSCC) cell line
origin: human tongue squamous cell carcinoma
growth condition: hypoxia (1% oxygen)
|
| Treatment protocol |
The Cal-27 cells were cultured under 20% O2 (normoxic) or 1% O2 (hypoxic) conditions, balanced with N2 in a 3-gas incubator.
|
| Growth protocol |
Cal-27 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum, 2mM L-glutamine, 25mM HEPES, and 100 units/ml penicillin and 100 ug/ml streptomycin in a humidified 5% CO2 atmosphere.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cells grown in monolayer 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 |
Hypo2
|
| 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 3 out of 6 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) |
| GSE84790 |
lncRNA expression profiles in OSCC cells cultured under normoxic and hypoxic conditions |
| GSE84807 |
Long noncoding RNA HAS2-AS1 mediates hypoxia-induced invasiveness of oral squamous cell carcinoma |
|
