|
| Status |
Public on May 21, 2019 |
| Title |
RKO siUHRF1-1 |
| Sample type |
genomic |
| |
|
| Source name |
RKO with UHRF1 siRNA1 plus mock
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RKO
sirna: UHRF1 siRNA1
genotype: UHRF1 depletion
agent: mock
|
| 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.
|
| 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 |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the standard phenol-chloroform method.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.
|
| Description |
3999547139_R05C01_Grn.idat
3999547139_R05C01_Red.idat
RKO with UHRF1 siRNA1 plus mock
RKO-siUHRF1-1
|
| Data processing |
BeadStudio software V2011.1
Signals were background subtracted and normalized to internal controls using GenomeStudio V2011.1 and Methylation Module 1.9.0.
|
| |
|
| Submission date |
Nov 02, 2017 |
| 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 |
GPL13534 |
| Series (2) |
| GSE106438 |
Analysis of DNA methylation in colorectal cancer RKO cells with UHRF1 depletion and HDAC inhibition |
| GSE106439 |
UHRF1 depletion and HDAC inhibition synergistically reactivate epigenetically silenced genes in colorectal cancer cells |
|
