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Status |
Public on Jan 17, 2014 |
Title |
SCCO-014 tumor vs. Normal ovary |
Sample type |
RNA |
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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).
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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).
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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.
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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.
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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 |
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