|
| Status |
Public on Jul 29, 2011 |
| Title |
miRNA OSE 665 |
| Sample type |
RNA |
| |
|
| Source name |
Healthy ovarian surface epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
tumor stage/grade: N/A
age at surgery: 84
|
| Treatment protocol |
Normal ovarian surface epithelial (OSE) cells were collected from ovaries at time of surgery using a Cytobrush ® Plus (Medscand) and immediately stabilized in RNAlater (Ambion) and stored at –20 degrees C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For miRNA extraction from normal ovarian surface epithelia, the cells were spun down and resuspended in lysis buffer from the mirVana miRNA Isolation Kit, and total RNA was extracted following the manufacturer's recommended protocol (Ambion, Austin, TX). The miRNA-enriched fraction of small RNAs was purified from total RNA by polyacrylamide gel electrophoresis using Ambion’s flashPAGE™ kits (Ambion Inc., Austin, TX).
|
| Label |
biotin
|
| Label protocol |
The 3’ ends of the RNA molecules were tailed and biotin-labeled using the mirVana™ miRNA Labeling Kit (Ambion Inc., Austin, TX). The kit’s dNTP mixture in the tailing reaction was replaced with a proprietary nucleotide mixture containing biotin-modified nucleotides (PerkinElmer, Waltham, MA).
|
| |
|
| Hybridization protocol |
Hybridization was performed according to Affymetrix-recommended procedures, except that the 20X GeneChip Eukaryotic Hybridization Control cocktail was omitted from the hybridization.
|
| Scan protocol |
Scanning was performed according to Affymetrix-recommended procedures. The fluorecence data is extracted at 1.4 micron pixel resolution using the Affymetrix 3000 7G scanner
|
| Description |
Ovarian surface epithelia brushing from ovaries described by pathology as within normal limits.
|
| Data processing |
For each probe, an estimated background value is subtracted that is derived from the median signal of a set of G-C-matched anti-genomic controls. Arrays within a specific analysis experiment were normalized together according to the variance stabilization method described by Huber et al. (Huber et al., 2002). Detection calls were based on a Wilcoxon rank-sum test of the miRNA probe signal compared to the distribution of signals from GC-content matched anti-genomic probes. A two-sample t-Test, with assumption of equal variance, was applied for statistical hypothesis testing. This test defined which probes are considered to be significantly differentially expressed based on a p-value of 0.01 and log2 difference ≥ 1.
|
| |
|
| Submission date |
Aug 02, 2010 |
| Last update date |
Nov 18, 2013 |
| Contact name |
Shubin Shahab |
| E-mail(s) |
shubin.shahab@gmail.com
|
| Organization name |
Georgia Institute of Technology
|
| Department |
Biology
|
| Lab |
McDonald
|
| Street address |
310 Ferst Drive
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30332 |
| Country |
USA |
| |
|
| Platform ID |
GPL9735 |
| Series (2) |
| GSE23383 |
miRNAs in ovarian cancer: A systems approach (miRNA data) |
| GSE23392 |
miRNAs in ovarian cancer: A systems approach |
|
| Relations |
| Reanalyzed by |
GSE52459 |
