|
| Status |
Public on Feb 20, 2019 |
| Title |
DMSO_shCTCF1_Rep2_RNA |
| Sample type |
RNA |
| |
|
| Source name |
Immortalized prostate epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Immortalized prostate epithelial cells
treatment: No knockdown control, vehicle treated, 5 days
|
| Treatment protocol |
Stable cell lines harboring doxycycline inducible shRNA targeting CTCF were maintained under selection with 1ug/ml puromycin on 10cm plates. Doxycycline or vehicle only (DMSO) was added to media at 2ug/ml, media and doxycycline were refreshed every 48 hours until harvest.
|
| Growth protocol |
Cells were grown in Ham's F12 Medium supplemented with 1% fetal bovine serum, 100 U/ml penicillin/streptomycin, 2mM L-glutamine, 0.1mM non-essential amino acids, 2.7mg/ml dextrose, 5microgram/ml human transferrin, 1microgram/ml hydrocortisone, 0.25U/ml human insulin, 10ng/ml cholera toxin, and 0.25% bovine pituitary extract. Cells were grown in 37C incubator at 5% CO2. Cells were harvested following 5 days of treatment, and proceeded to RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the PerfectPure RNA Tissue Kit (5prime) according to manufacturer's instructions. Quality assesment was conducted using an Agilent RNA Nanochip and by a Nanodrop spectrophotometer (Thermo).
|
| Label |
Biotin
|
| Label protocol |
Single-stranded cDNA was generated from 15ug of total RNA with the Affymetrix WT Plus Expression kit and then fragmented and labeled with the Affymetrix WT Terminal Labiling Kit according to manufacturer's protocols.
|
| |
|
| Hybridization protocol |
Samples were hybridized to the Human Transcriptome 2.0 Array (Affymetrix) and scanned at the University of Wisconsin-Madison Biotechnology Center.
|
| Scan protocol |
Gene chips were post processed on the AFX Fluidics 450 Station, and Chips were scanned on the GC3000 G7 Scanner (Serial #50208130)
|
| Description |
Uninduced control rep 2
|
| Data processing |
Raw data were processed with the Affymetrix Command Console version 4.0.0.1567G (Affymetrix) for background correction and normalization. Data analysis were performed using the Transcriptome Analysis Console v3.0 (Affymetrix). RMA expression value (Log2 transformed) derived from Expression Console Software
|
| |
|
| Submission date |
Jan 10, 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 |
GPL17586 |
| Series (2) |
| GSE93363 |
Expression data from short hairpin RNA mediated CTCF knockdown in human prostate epithelial cells |
| GSE93364 |
DNA methylation and gene expression after decreased CTCF expression in human prostate epithelial cells |
|
