|
| Status |
Public on Dec 30, 2018 |
| Title |
colorectal cancer HCT/neg3 |
| Sample type |
RNA |
| |
|
| Source name |
HCT116 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: colorectal cancer cell line
treatment: miRNA-negative control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using miRNeasy mini kit (Qiagen) and RNA extraction reagent from liquid sample kit (Toray Industries, Inc.) in accordance with the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
cDNA and Amino Allyl aRNA were synthesized by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc.
|
| |
|
| Hybridization protocol |
Hybridized for 16h at 37C with rotary shake (250rpm). Hybridization buffer and washing protocol were followed by the protocol of the 3D-Gene® mRNA oligo chip kit.
|
| Scan protocol |
3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).
|
| Description |
HCT/neg3
mRNA
|
| Data processing |
Mean and standard deviation (SD) of the 5% trimmed signals of the negative controls were calculated. Signals over mean+2SD of the negative controls were subtracted with the mean of the negative controls. The undetected signal was replaced with the value that was the least signal intensity on each DNA chip minus 0.1 in log2 scale followed by quantile normalization.
|
| |
|
| Submission date |
May 10, 2018 |
| Last update date |
Dec 30, 2018 |
| Contact name |
Atsuko Mizoguchi |
| E-mail(s) |
[email protected]
|
| Organization name |
Toray Industries, Inc.
|
| Department |
New Frontiers Research Laboratories
|
| Street address |
6-10-1, Tebiro
|
| City |
Kamakura |
| State/province |
Kanagawa |
| ZIP/Postal code |
248-8555 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13915 |
| Series (2) |
| GSE114316 |
MicroRNA-8073: Tumor suppressor and potential therapeutic treatment [mRNA] |
| GSE114318 |
MicroRNA-8073: Tumor suppressor and potential therapeutic treatment |
|
