|
| Status |
Public on Mar 23, 2021 |
| Title |
HCT116, DUSP4 siRNA #1 |
| Sample type |
RNA |
| |
|
| Source name |
Colorectal cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Colorectal cancer cell line HCT116
treatment: DUSP4 siRNA#1
genotype: DUSP4 knockdown
|
| Growth protocol |
All cell lines were cultured in accordance with the supplier's instructions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA for expression analysis was extracted using an RNeasy Mini kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Cy3-labeled cRNA targets were generated using Quick Amp Labeling Kit, one-color (Agilent Technologies).
|
| |
|
| Hybridization protocol |
Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).
|
| Scan protocol |
Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).
|
| Description |
Cultured in accordance with the supplier's instructions. Total RNA for expression analysis was extracted using an RNeasy Mini kit (Qiagen).
|
| Data processing |
Feature Extraction software (Version 9.1, Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis. Analysis of the microarray images was performed with Genespring 7.3.1 Software (Agilent Technologies).
The signal intensities of probe set data were median-normalized per chip, followed by filtering based on signal intensity and flagged values.The genes regulated by DUSP4 were identified using following filters: for 419 upregulated genes, (DUSP4 siRNA#1 ≥ 500, DUSP4 siRNA#1/control siRNA ≥ 1.6) and (DUSP4 siRNA#2 ≥ 500, DUSP4 siRNA#2/control siRNA ≥ 1.6), for 291 downregulated genes, (control siRNA ≥ 500, DUSP4 siRNA#1/control siRNA ≤ 0.625) and (control siRNA ≥ 500, DUSP4 siRNA#2/control siRNA ≤ 0.625).
|
| |
|
| Submission date |
Feb 19, 2020 |
| Last update date |
Mar 23, 2021 |
| Contact name |
Naoki Hijiya |
| E-mail(s) |
hijiya@oita-u.ac.jp
|
| Phone |
1975865693
|
| Organization name |
Oita University
|
| Department |
Medicine
|
| Lab |
Molecular pathology
|
| Street address |
1-1, Idaigaoka Hasama-machi
|
| City |
Yufu |
| State/province |
Oita |
| ZIP/Postal code |
879-5593 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13497 |
| Series (1) |
| GSE145511 |
Identification of genes regulated by DUSP4 |
|
