|
| Status |
Public on Feb 20, 2019 |
| Title |
5MC_shCTCF1_DMSO_Rep2 |
| Sample type |
genomic |
| |
|
| Source name |
Immortalized prostate epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Immortalized prostate epithelial cells
ctcf knockdown: No knockdown control
sample fraction: 5mC antibody enriched
|
| Treatment protocol |
Controls were treated with vehicle only (DMSO) for 5 days, CTCF knockdown samples were treated with 2 micrograms/milliliter of Doxycycline to induce shRNA targeting CTCF for 5 days.
|
| Growth protocol |
Cell lines were grown according to standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using Qiagen Dneasy blood and tissue kit according to manufacturer's protocols. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.
|
| Label |
Biotin
|
| Label protocol |
Labling was performed according to manufacturer's protocols (CytoScan HD Array Manual)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, methylated DNA was immunoprecipitated by 5mC antibody and purified. Input and methylated DNA samples were PCR amplified, fragmented, labeled, and hybridized to the array individually according to manufacturer's protocols.
|
| Scan protocol |
The arrays were washed using Affymetrix fluidics stations and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to CytoScanHD_Array
|
| Data processing |
Array image was acquired using Affymetrix GeneChip Operating Software (GCOS version 1.4). Raw intensity files were extracted from .CEL files using Affymetrix Power Tools. Input subtraction was used to normalize for copy number specific effects. Input subtracted Log2 intensity data was used for comparison of methylated DNA enrichment. Statistical analysis was performed using LIMMA to identify regions of significantly altered enrichment.
|
| |
|
| Submission date |
Jan 09, 2017 |
| Last update date |
Feb 20, 2019 |
| Contact name |
Nathan Damaschke |
| Organization name |
University of Wisconsin
|
| Department |
Urology
|
| Lab |
Jarrard
|
| Street address |
1111 Highland Ave Room 7048
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL16131 |
| Series (2) |
| GSE93328 |
Decreased CTCF Expression Directs DNA Hypermethylation Events in Cancer |
| GSE93364 |
DNA methylation and gene expression after decreased CTCF expression in human prostate epithelial cells |
|
