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Sample GSM573600 Query DataSets for GSM573600
Status Public on Jul 29, 2011
Title miRNA CEPI 551
Sample type RNA
 
Source name Laser captured microdissected ovarian cancer epithelial cells
Organism Homo sapiens
Characteristics tumor stage/grade: IIIc/IV/3
age at surgery: 59
Treatment protocol Following pathological verification, a serous papillary epithelial cancer sample was embedded in cryomatrix (Shandon). Seven micron frozen sections were cut and attached to uncharged microscope slides for each sample. Immediately following dehydration and staining (HistoGene, LCM Frozen Section Staining Kit, Arcturus), slides were processed in an Autopix‘ instrument (Arcturus) for laser capture microdissection (LCM) of cells to CapSure Macro LCM Caps. Approximately 30,000 epithelia were collected from each cancer sample.
Extracted molecule total RNA
Extraction protocol Fresh frozen tissues from tumors were cut into seven-micron sections, applied to non-charged slides, then fixed in 75% ethanol for 30 seconds, stained and dehydrated using the HistoGene LCM Frozen Section Staining Kit (Arcturus, Mountain View, CA). LCM was performed with an AutoPix Automated Laser Capture Microdissection System using the CapSure Macro Caps (Arcturus, Mountain View, CA). Approximately 10,000 cells were captured on each of 5-6 caps per sample. MiRNA was extracted from captured cells using the mirVana miRNA Isolation Kit (Ambion, 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 Serous ovarian tumor tissues were placed in cryotubes and immediately (<1 minute) frozen in liquid nitrogen following resection.
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

Data table header descriptions
ID_REF
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 -2.36263316 30 0.5 0
hsa-miR-615_st1 -2.26698392 31 0.5 0
hsa-asg-2532_st1 -2.26698392 31 0.5 0
hsa-miR157_st2 0.877105821 29 0.5 0
hsa-asg-1081_st2 1.075777457 46 0.5 0
hsa-asg-4835_st1 -0.936407737 40 0.5 0
hsa-asg-13445_st1 -0.408399663 42 0.5 0
mmu-miR-140-_st1 3.763693094 43 0.200960306 0
hsa-asg-2744_st1 -2.36263316 30 0.5 0
hsa-miR235_st1 -2.164762623 32 0.5 0
hsa-asg-6830_st1 -1.808278127 35 0.5 0
hsa-asg-10926_st2 2.456957993 32 0.158021749 0
hsa-asg-325_st2 5.20050332 67 0.048669054 1
hsa-asg-3582_st2 3.497288967 57 0.385029156 0
hsa-asg-4690_st1 -1.93667439 34 0.5 0
hsa-miR-324-3p_st1 -1.87382978 31 0.5 0
hsa-asg-13931_st2 2.217123216 32 0.371609877 0
hsa-asg-1106_st1 -2.36263316 30 0.5 0
hsa-miR-608_st2 -1.047672672 29 0.5 0
hsa-asg-1616_st2 5.005335795 63 0.062182835 0

Total number of rows: 14215

Table truncated, full table size 583 Kbytes.




Supplementary file Size Download File type/resource
GSM573600.CEL.gz 207.6 Kb (ftp)(http) CEL
Processed data included within Sample table

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