|
| Status |
Public on Aug 13, 2013 |
| Title |
HSC-3 cells (control) vs. HSC-3-5 cells (high invasive) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Control HSC-3-0 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HSC-3 (JCRB0623)
tissue: tongue
|
| Treatment 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.
|
| Growth protocol |
HSC-3 cells which metastasized to the lymph nodes 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 |
RNA from HSC-3 cells was labeled by Cy3 and RNA from HSC-3-5 cells was labeled by Cy5. 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.
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| |
|
| Channel 2 |
| Source name |
HSC-3-5 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: drived from the parental HSC-3 (JCRB0623)
tissue: tongue
|
| Treatment 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.
|
| Growth protocol |
HSC-3 cells which metastasized to the lymph nodes 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 |
cy5
|
| Label protocol |
RNA from HSC-3 cells was labeled by Cy3 and RNA from HSC-3-5 cells was labeled by Cy5. 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 or Cy5 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.
|
| |
|
| |
| Hybridization protocol |
0.3 μg of Cy-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 a Agilent SurePrint G3 Human GE 8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.
|
| 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 and 625 nm for Cy5.
|
| Description |
1 X 10^7cells of total RNA was extracted after 24hours subculture
|
| Data processing |
Agilent Feature Extraction Software (v10.5.1), an image analysis and normalization software, is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.
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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) |
| GSE39723 |
HSC-3 cells (control) vs. HSC-3-5 cells [cell line] |
| GSE39729 |
HSC-3 cells (control) vs. HSC-3-5 cells |
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