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Sample GSM573604 Query DataSets for GSM573604
Status Public on Jul 29, 2011
Title miRNA OSE 783
Sample type RNA
Source name Healthy ovarian surface epithelial cells
Organism Homo sapiens
Characteristics tumor stage/grade: N/A
age at surgery: 52
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
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
Reanalyzed by GSE52459

Data table header descriptions
VALUE vst normalized signal intensity
Raw PM
Detection p-value
Detection Call

Data table
ID_REF VALUE Raw PM Detection p-value Detection Call
hsa-asg-10812_st1 3.345539705 40 0.417251161 0
hsa-miR-615_st1 4.029336025 44 0.330412186 0
hsa-asg-2532_st1 5.908679665 72 0.163057506 0
hsa-miR157_st2 7.617304097 154 0.044406197 1
hsa-asg-1081_st2 6.181912498 80 0.148091548 0
hsa-asg-4835_st1 5.663410745 66 0.178970602 0
hsa-asg-13445_st1 4.923668256 53 0.219745864 0
mmu-miR-140-_st1 7.160751558 120 0.067262398 0
hsa-asg-2744_st1 5.749874773 68 0.168255642 0
hsa-miR235_st1 -0.782017255 31 0.5 0
hsa-asg-6830_st1 -0.782017255 31 0.5 0
hsa-asg-10926_st2 5.523172179 57 0.05232754 1
hsa-asg-325_st2 7.011096579 110 0.043898679 1
hsa-asg-3582_st2 3.547932706 41 0.392959881 0
hsa-asg-4690_st1 2.83737593 38 0.458400246 0
hsa-miR-324-3p_st1 -0.308448154 32 0.5 0
hsa-asg-13931_st2 5.791241647 63 0.047856992 1
hsa-asg-1106_st1 4.029336025 44 0.330412186 0
hsa-miR-608_st2 3.112095003 35 0.348650544 0
hsa-asg-1616_st2 7.045720118 113 0.044406197 1

Total number of rows: 14215

Table truncated, full table size 577 Kbytes.

Supplementary file Size Download File type/resource
GSM573604.CEL.gz 196.7 Kb (ftp)(http) CEL
Processed data included within Sample table

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