|
| Status |
Public on Dec 31, 2011 |
| Title |
blood_cancer1_family43_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
cancer status: Prostate cancer patient
diagnosis age: 50y 9m
gleason score: 6
cell type: lymphoblastoid cell line
individual: cancer1_family43
|
| Treatment protocol |
The samples were not treated.
|
| Growth protocol |
The lymphoblastoid cell lines were derived by Epstein-Barr virus transformation of peripheral mononuclear leukocytes from patients and their healthy brothers. Lymphoblastoid cell lines were grown in RPMI-1640 medium (Lonza, Walkersville, MD, USA) supplemented with 10% fetal bovine serum (Sigma-Aldrich, St. Louis, MO, USA) and antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells with Trizol according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA, USA). RNA yields were quantified using an ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
|
| Label |
Cy3
|
| Label protocol |
100 ng of total RNA was used as a starting material, and miRNAs were labeled with Cy3 using the Agilent miRNA Labeling Kit according to the instructions of the manufacturer.
|
| |
|
| Hybridization protocol |
Labeled and purified RNA was dried down in speedvac (1h +45C). RNA was resuspended in 18 ul of H2O. 4.5ul of 10x Blocking agent and 22.5 ul 2x Hybrdization buffer was added. The hybridization assembly was mounted and the arrays were hybridized for 20h at +55C.
|
| Scan protocol |
The scanned images were analyzed with Feature Extraction Software 9.5.1. (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Outliers were excluded.
|
| Description |
miRNA expression in lymphoblastoid cells
|
| Data processing |
For data analysis, low quality samples and non-expressed miRNAs were first removed. Inside every family the directional distance of healthy individuals from patients was calculated. The distance used here was based on Kendal’s tau (distance = (1-tau)/2) and the distance between clusters was computed using Ward’s method. By decomposing Kendal’s tau into each miRNA’s contribution the distance induced by every miRNA can be quantified separately. The direction of this distance inside every family is marked positive if the average rank miRNA expression for patients is higher than for healthy individuals and negative if the average rank miRNA expression for healthy individuals is higher than for patients. The overall directional distance for every miRNA is obtained by summing up these directional distances over all families. Then the permutation p-value was computed by permuting healthy individuals and patients randomly inside every family, computing the overall directional distance, repeating this many times and the final permutation p-value is the proportion of these permuted distances higher or lower than the original distance. The analysis was not performed on probe level, but on miRNA level with the help of ranks and gTotalGeneSignal.
|
| |
|
| Submission date |
Sep 17, 2010 |
| Last update date |
Dec 31, 2011 |
| Contact name |
Henna Mattila |
| E-mail(s) |
henna.mattila@uta.fi
|
| Phone |
+358335516666
|
| Organization name |
University of Tampere
|
| Department |
Institute of Medical Technology
|
| Lab |
Laboratory of Cancer Genetics
|
| Street address |
Biokatu 8
|
| City |
Tampere |
| ZIP/Postal code |
33520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL7731 |
| Series (2) |
| GSE24201 |
miRNA profiling of HPCX1 linked prostate cancer patients and their healthy brothers |
| GSE24205 |
HPCX1 linked prostate cancer |
|
