|
| Status |
Public on Jan 18, 2017 |
| Title |
2D |
| Sample type |
RNA |
| |
|
| Source name |
Cell cultured on tissue culture polystyrene plates
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HT29
cell type: colon cancer cell line
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the RNeasy Mini Purification kit (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 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C 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 with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner using one color scan setting for 8x60kv2 array slides.
|
| Data processing |
The scanned images were analyzed with R using limma package.
|
| |
|
| Submission date |
Jan 17, 2017 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Keisuke Sekine |
| Organization name |
National Cancer Center Research Institute, Japan
|
| Department |
Graduate School of Medicine
|
| Lab |
Laboratory of Cancer Cell Systems
|
| Street address |
5-1-1 Tsukiji
|
| City |
Chuo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
104-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16699 |
| Series (1) |
| GSE93704 |
Chitosan promotes cancer progression and stem cell properties through Wnt signaling in colon and hepatocellular carcinoma cells |
|
| Relations |
| Reanalyzed by |
GSE113533 |
