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Sample GSM1208937 Query DataSets for GSM1208937
Status Public on Jan 17, 2014
Title SCCO-014 tumor vs. Normal ovary
Sample type RNA
 
Channel 1
Source name Fresh frozen SCCO primary tumor
Organism Homo sapiens
Characteristics tissue: Fresh frozen SCCO primary tumor
diagnosis: Small cell carcinoma of the ovary
age at diagnosis: 33
ethnicity: African American
hypercalcemia: Yes
figo stage: IIIC
tumor size: Unknown
Extracted molecule total RNA
Extraction protocol Tumor homogenization was conducted with a Covaris S-2 tissue disrupter (Covaris; Woburn, MA) followed by additiona of TRIzol reagent (Invitrogen; Carlsbad, CA). Total RNA was purified using the RNeasy micro kit (Qiagen; Valencia, CA) following the manufacturer's instructions. For the reference, normal ovarian RNA from 2 different individuals (32 and 37 years of age) was obtained from OriGene (Rockville, MD), catalog numbers CR562102, CR561549). The RNA integrity and purity of all samples was measured using a 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA) and a Nanodrop ND-1000 Spectrophotometer (Nanodrop; Wilmington, DE). RIN# for all RNAs were >8.
Label Cy3
Label protocol 200 ng of RNA from each tumor sample were labeled with Cy3 using Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies; Palo Alto, CA) following manufacturer's instructions. For the reference, 100 ng of RNA from each of the 2 commerical normal ovary samples were combined and labeled with Cy5 using Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies; Palo Alto, CA) following manufacturer's instructions. Labeling efficiency was measured with a Nanodrop ND-1000 Spectrophotometer (Nanodrop; Wilmington, DE).
 
Channel 2
Source name Pool of 2 commercial normal ovary RNA samples
Organism Homo sapiens
Characteristics age: 32, 37
case diagnosis: Endometriosis, endometriosis
supplier: OriGene Technologies
catalog numbers: CR562102, CR561549
tissue: Normal ovary unaffected by endometriosis
Extracted molecule total RNA
Extraction protocol Tumor homogenization was conducted with a Covaris S-2 tissue disrupter (Covaris; Woburn, MA) followed by additiona of TRIzol reagent (Invitrogen; Carlsbad, CA). Total RNA was purified using the RNeasy micro kit (Qiagen; Valencia, CA) following the manufacturer's instructions. For the reference, normal ovarian RNA from 2 different individuals (32 and 37 years of age) was obtained from OriGene (Rockville, MD), catalog numbers CR562102, CR561549). The RNA integrity and purity of all samples was measured using a 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA) and a Nanodrop ND-1000 Spectrophotometer (Nanodrop; Wilmington, DE). RIN# for all RNAs were >8.
Label Cy5
Label protocol 200 ng of RNA from each tumor sample were labeled with Cy3 using Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies; Palo Alto, CA) following manufacturer's instructions. For the reference, 100 ng of RNA from each of the 2 commerical normal ovary samples were combined and labeled with Cy5 using Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies; Palo Alto, CA) following manufacturer's instructions. Labeling efficiency was measured with a Nanodrop ND-1000 Spectrophotometer (Nanodrop; Wilmington, DE).
 
 
Hybridization protocol 1230 ng of labeled tumor RNA and 825 ng of labeled reference RNA were prepared and hybridized to Agilent 4x44K (V2) gene expression microarrays following manufacturer protocols (Agilent Technologies; Palo Alto, CA).
Scan protocol Slides were washed with Agilent's Gene Expression Wash Buffers (Part Number 5188-5327) following Agilent's protocol and scanned at 5 μm using an Agilent Microarray Scanner (model G2505B) in an ozone-controlled environment.
Data processing Agilent Feature Extraction software (v10.5) was used for background subtraction and normalization. Array control features and control targets were removed. Data transformed from Log10 to Log2.
 
Submission date Aug 14, 2013
Last update date Jan 17, 2014
Contact name Heather E. Cunliffe
Organization name University of Otago, Dunedin School of Medicine
Department Department of Pathology
Street address P O Box 913
City Dunedin
State/province Otago
ZIP/Postal code 9054
Country New Zealand
 
Platform ID GPL10332
Series (1)
GSE49887 Small Cell Carcinoma of the Ovary (SCCO) vs. Normal Ovary

Data table header descriptions
ID_REF
VALUE Normalized Log2 Ratio (Cy3/Cy5) representing test/reference

Data table
ID_REF VALUE
12 -4.087661554
13 0.61328824
14 -1.757019225
15 -0.218716891
16 1.486017318
17 0
18 0.43646439
19 0.769939528
20 0.793369419
21 -1.971069982
22 0.30857864
23 1.324988211
24 2.157709074
25 -1.27235014
26 0.421547799
27 -5.556881959
28 0.553632585
29 0.46956147
30 -1.227243272
31 -3.169442924

Total number of rows: 43118

Table truncated, full table size 709 Kbytes.




Supplementary file Size Download File type/resource
GSM1208937_SCCO_014_vs_Normal.txt.gz 15.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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