|
| Status |
Public on May 21, 2019 |
| Title |
RKO siCONT plus TSA replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
RKO with control siRNA plus TSA replicate1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RKO
cell type: colorectal cancer
sirna: control
genotype: control
drug: Trichostatin A
|
| Treatment protocol |
RKO cells were transfected with a control siRNA (Thermo Fisher Scientific) or siRNAs targeting UHRF1 (Thermo Fisher Scientific) using using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and incubated for 72 h. Cells were then treated with mock (ethanol) or 300 nM Trichostatin A (TSA) for additional 24 h. Alternatively, RKO cells were treated with 1 microM 5-aza-2'-deoxycytidine for 72 h.
|
| Growth protocol |
RKO cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a TRIZOL reagent (Invitrogen).
|
| Label |
Cy3
|
| Label protocol |
Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.
|
| |
|
| Hybridization protocol |
Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.
|
| Scan protocol |
Array was scanned with an Agilent G2565BA Microarray Scanner.
|
| Description |
RKO with control siRNA plus TSA replicate1
|
| Data processing |
Agilent Feature Extraction Software (v 10.7) was used for background subtraction.
|
| |
|
| Submission date |
Apr 25, 2018 |
| Last update date |
May 21, 2019 |
| Contact name |
Hiromu Suzuki |
| E-mail(s) |
hsuzuki@sapmed.ac.jp
|
| Phone |
+81-11-611-2111
|
| Organization name |
Sapporo Medical University
|
| Department |
Department of Molecular Biology
|
| Street address |
S1, W17, Chuo-ku
|
| City |
Sapporo |
| State/province |
Hokkaido |
| ZIP/Postal code |
060-8556 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16699 |
| Series (2) |
| GSE106439 |
UHRF1 depletion and HDAC inhibition synergistically reactivate epigenetically silenced genes in colorectal cancer cells |
| GSE113664 |
Analysis of gene expression in colorectal cancer RKO cells with UHRF1 depletion and HDAC inhibition |
|
