|
| Status |
Public on Aug 13, 2013 |
| Title |
HSC-3 subcutaneous tumor |
| Sample type |
RNA |
| |
|
| Source name |
HSC-3 tumor, subcutaneous tumor, 6 weeks
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: tumor of HSC-3
age: 6 weeks of tumor on SCID mice flank
|
| Treatment protocol |
HSC-3 and HSC-3-5 oral cancer cells (2.5 × 105/ 50 μL) were respectively mixed with 50 μL matrigel and subcutaneously injected into SCID mice. After 6 weeks, total RNA was extracted from the tumor tissue on SCID flank.
|
| Growth protocol |
Sub-populations from HSC-3 cells were base on their differential invasiveness to be isolated via using Transwell matrigel coated plates. Briefly, transwell matrigel invasion assay were performed to sub-lines selection of HSC-3 cells. After incubation for 72 hours, we harvested the cells that migrated through the upper chambers with matrigel coated or attached to the lower chambers. Then we amplified the cells that we harvested for second-round selection. We named the sub-line of the first-round selection cells as HSC-3-1. Following that other sub-lines from 2, 3, 4, and 5 rounds of selection were named as HSC-3-2, -3, -4, and -5, respectively. Both HSC-3 and HSC-3-5 cells were maintained in Eagle's minimal essential medium with 10% calf serum supplemented.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.
|
| |
|
| Hybridization protocol |
0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Human GE 8×60K microarray (Agilent Technologies, USA) at 65°C for 17 hours.
|
| Scan protocol |
After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.
|
| Description |
Gene expression of HSC-3 tumor after 6 weeks inoculated
|
| Data processing |
Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.
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| |
|
| Submission date |
Jul 30, 2012 |
| Last update date |
Aug 13, 2013 |
| Contact name |
Yi-Ting Chen |
| Organization name |
National Cheng Kung University
|
| Department |
Department of Medical Laboratory Science and Biotecnology
|
| Lab |
Dr. Chuan Fa Chang
|
| Street address |
No. 1 University Road
|
| City |
Tainan |
| ZIP/Postal code |
70101 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL14550 |
| Series (2) |
| GSE39726 |
HSC-3 cells (control) vs. HSC-3-5 cells [subcutaneous tumor] |
| GSE39729 |
HSC-3 cells (control) vs. HSC-3-5 cells |
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