|
| Status |
Public on Aug 25, 2015 |
| Title |
DO2 |
| Sample type |
RNA |
| |
|
| Source name |
not treated DU145 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: DU145
status: metastasis
tissue: brain
developmental stage: prostate adenocarcinoma metastatic to the brain
cell type: 90 times in vitro passed epithelial cell culture
treated with: none (untreated)
|
| Treatment protocol |
untreated or treated with 5nM Capridine
|
| Growth protocol |
DU145 cell culture
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)
|
| Label |
Cy5
|
| Label protocol |
Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.
|
| |
|
| Hybridization protocol |
825 ng from each of the Cy3 or Cy5 labeled samples from two cell dishes were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.
|
| Scan protocol |
The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.
|
| Description |
raw data file: DO1_2-US83300186_252665223519_S01_GE2_1105_Oct12_1_4.txt
Gene expression in untreated DU145 cell culture
not treated DU145 cells_Replicate 2
|
| Data processing |
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 11.5.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
Normalized log2 ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal
|
| |
|
| Submission date |
Aug 24, 2015 |
| Last update date |
Aug 25, 2015 |
| Contact name |
Dumitru Andrei Iacobas |
| E-mail(s) |
daiacobas@pvamu.edu
|
| Phone |
936-261-9926
|
| Organization name |
Prairie View A&M University
|
| Department |
Undergraduate Medical Academy
|
| Lab |
Personalized Genomics
|
| Street address |
Ann Preston St
|
| City |
Prairie View |
| State/province |
TX |
| ZIP/Postal code |
77446 |
| Country |
USA |
| |
|
| Platform ID |
GPL10332 |
| Series (1) |
| GSE72333 |
Remodeling of major genomic fabrics and their interplay in Capridine-treated DU145 classic human prostate cancer |
|
