|
| Status |
Public on Mar 08, 2013 |
| Title |
DKO1-2 |
| Sample type |
RNA |
| |
|
| Source name |
DKO1 Cell Line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: control
cell line: DKO1 Cell Line
|
| Treatment protocol |
Cells were treated with 0.3 uM Aza and harvested after 72 hours or with 1 uM SAHA treatment and harvested after 24hours
|
| Growth protocol |
Cells were grown under standard conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using standard TRIzol procedure.
|
| Label |
biotin
|
| Label protocol |
Standard Illumina labeling protocol
|
| |
|
| Hybridization protocol |
RNA was amplified, fragmented and hybridized to the Illumina bead array using standard Illumina protocols
|
| Scan protocol |
Beadchips were imaged using Illumina BeadArray Reader using standard recommended Illumina scanner setting.
|
| Description |
male, derivative of HCT116, engineerd disruption of DNA methyltransferase DNMT1 and DNMT3B, control
|
| Data processing |
Raw signal intensities for each probe were obtained using Illumina Beadstudio data analysis software and imported to the Bioconductor lumi package for data transformation and normalization. Probes with all samples ‘‘absent’’ (near or below background levels) were filtered. Loess normalization was performed
|
| |
|
| Submission date |
Jan 29, 2013 |
| Last update date |
Mar 08, 2013 |
| Contact name |
Kurinji Pandiyan |
| Organization name |
University of Southern California
|
| Department |
Department of Urology - Norris Comprehensive Cancer Center
|
| Street address |
1441 Eastlake Avenue NOR 7344
|
| City |
Los Angeles |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL10904 |
| Series (2) |
| GSE38858 |
AcceSssIble Assay to Study the Chomatin Accessibility and DNA Methylation |
| GSE43852 |
Functional DNA methylation is accompanied by chromatin accessibility [gene expression] |
|
