|
| Status |
Public on Oct 12, 2012 |
| Title |
Human oral squamous cell carcinoma cell line 1-2 |
| Sample type |
RNA |
| |
|
| Source name |
Human oral squamous cell carcinoma_HSC-4
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HSC-4
cell type: oral squamous cell carcinoma cells
|
| Treatment protocol |
Human oral squamous cell carcinoma cell lines HSC-4 and OSC-19 were cultured in RPMI1640 and Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FBS. All cell lines were maintained under 5% CO2 at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.And RNA was prepared using the , RNAeasy mini (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using the One-Color Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.65 ug of Cy3-labelled cRNA was fragmented following the manufacturers instructions. On completion of the fragmentation reaction, 60 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Whole Genome Oligo Microarrays ver2(G4845A) for 17 hours at 65℃in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at room temperature GE Wash buffer 2 (Agilent), then dried immediately by air spray.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10% ).
|
| Description |
HSC-4 2
|
| Data processing |
The scanned images were analyzed with Feature Extraction software v.10.10.1.1 (Agilent).
|
| |
|
| Submission date |
Oct 11, 2012 |
| Last update date |
Oct 19, 2012 |
| Contact name |
Osamu Nagano |
| E-mail(s) |
osmna@sb3.so-net.ne.jp
|
| Phone |
+81-3-5363-3983
|
| Fax |
+81-3-5363-3982
|
| Organization name |
Keio University School of Medicine
|
| Department |
Institute for Advanced Medical Research
|
| Lab |
Division of Gene Regulation
|
| Street address |
３５ Shinanomachi
|
| City |
Tokyo |
| State/province |
DDS PhD |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13497 |
| Series (1) |
| GSE41495 |
Gene expression analysis of human oral squamous cell carcinoma cell lines (HSC-4, OSC19) |
|
