|
| Status |
Public on May 21, 2019 |
| Title |
DLD1 siUHRF1-1 plus TSA |
| Sample type |
genomic |
| |
|
| Source name |
DLD1 with UHRF1 siRNA1 plus TSA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DLD1
sirna: UHRF1 siRNA1
genotype: UHRF1 depletion
agent: Trichostatin A
|
| Treatment protocol |
DLD1 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 48 h. Cells were then treated with mock (ethanol) or 300 nM Trichostatin A (TSA) for additional 24 h.
|
| Growth protocol |
DLD1 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 |
9682764154_R05C01_Grn.idat
9682764154_R05C01_Red.idat
DLD1 with UHRF1 siRNA1 plus TSA
DLD1-siUHRF1-1-TSA
|
| 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) |
| GSE106437 |
Analysis of DNA methylation in colorectal cancer DLD1 cells with UHRF1 depletion and HDAC inhibition |
| GSE106439 |
UHRF1 depletion and HDAC inhibition synergistically reactivate epigenetically silenced genes in colorectal cancer cells |
|
