|
| Status |
Public on Jan 14, 2014 |
| Title |
localized CaP_P396 |
| Sample type |
RNA |
| |
|
| Source name |
Human urine
|
| Organism |
Homo sapiens |
| Characteristics |
disease: localized CaP
|
| Treatment protocol |
A total 14 urines from patients with CaP (7 localized and 7 advanced stage) and 5 of BPH controls were used for miRNA array analysis.
|
| Growth protocol |
19 candidate urines (prostate cancer, CaP, patients and non-cancer subjects with benign prostatic hyperplasia, BPH) were selected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RecoverAllTM Total Nucleic Acid Isolation kit (Life Technologies, Carlsbad, CA) according to the protocol of the manufacturer. RNA quantity and integrity were examined by RNA 6000 Pico Chip Kit (Agilent Technologies, Santa Clara, CA) on Agilent 2100 Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
400 ng of total RNA was labeled with cyanine 3-pCp using the Agilent miRNA Complete Labeling kit and hybridized to the array according to the manufacturer’s protocol.
|
| |
|
| Hybridization protocol |
After purification, labeled samples were resuspended with Gene Expression Blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s Human miRNA Microarray (60K, Release 16.0) and hybridized at 55 °C for 20 h with 20 rpm rotating in Agilent Hybridization Oven. The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology).
|
| Scan protocol |
The hybridization images were analyzed by Agilent DNA microarray Scanner.
|
| Description |
miRNA expression in the localized CaP 396
|
| Data processing |
Feature Extraction software (version 10.10.1.1) was used for data extraction from raw microarray image files using the miRNA_105_Dec08 FE protocol. Background intensity and feature nonuniform outliers were removed by standard procedures. Data visualization and analysis were performed with GeneSpring GX (version 7.3) software (Agilent Technologies). Signal cut-off measurements were less than 0.01, and normalized to 75th percentile of signal intensity to standardize each chip for cross-array comparison. Differentially expressed miRNAs were identified using a Student’s two-sample t-test with p values cut off by 0.05 and fold change more than 2.0. One-way ANOVO was used to analyze the correlation between the expression levels of miRNAs and clinic-pathological features of the patients.
The normalized ratios were calculated by dividing the average of CaP channel intensity (localized CaPs or advanced CaPs) by the average of normalized control channel intensity (BPH).
|
| |
|
| Submission date |
Jan 13, 2014 |
| Last update date |
Jan 14, 2014 |
| Contact name |
Jung Min Kim |
| E-mail(s) |
jmkim2010@korea.com
|
| Phone |
82-10-3459-4776
|
| Organization name |
NAR Center, Inc. & Genoplan, Inc.
|
| Department |
Department of Health Genomics
|
| Lab |
Genetics & Genomics
|
| Street address |
Gangnam-gu Teheran-ro 216
|
| City |
Seoul |
| ZIP/Postal code |
06221 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL15159 |
| Series (1) |
| GSE54010 |
miRNA expression profiles in the 19 candidate urines (prostate cancer, CaP, patients and non-cancer subjects with benign prostatic hyperplasia, BPH) |
|
