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Status |
Public on Jan 17, 2014 |
Title |
Serous ovarian tumor C008 vs. 19 OVCA tumor pool |
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: Papillary serous adenocarcinoma age at diagnosis: 40 ethnicity: European figo stage: IIIC grade: 3 hypercalcemia: Not Applicable excision to snap freeze (min): 23
|
Treatment protocol |
Primary ovarian tumor was preserved from chemo-naïve patients at the time of diagnostic surgery.
|
Extracted molecule |
total RNA |
Extraction protocol |
Tumor homogenization was conducted with a Covaris S-2 tissue disrupter (Covaris; Woburn, MA) followed by addition of TRIzol reagent (Invitrogen; Carlsbad, CA). Total RNA was purified using the RNeasy micro kit (Qiagen; Valencia, CA) following the manufacturer's instructions. 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 >7.5
|
Label |
Cy3
|
Label protocol |
250 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, 200 ng of RNA from each of the 19 tumor samples were combined and labeled in batches of 500 ng 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 all 19 tumors analyzed
|
Organism |
Homo sapiens |
Characteristics |
tissue: Pool of all 19 tumors analyzed
|
Treatment protocol |
Primary ovarian tumor was preserved from chemo-naïve patients at the time of diagnostic surgery.
|
Extracted molecule |
total RNA |
Extraction protocol |
Tumor homogenization was conducted with a Covaris S-2 tissue disrupter (Covaris; Woburn, MA) followed by addition of TRIzol reagent (Invitrogen; Carlsbad, CA). Total RNA was purified using the RNeasy micro kit (Qiagen; Valencia, CA) following the manufacturer's instructions. 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 >7.5
|
Label |
Cy5
|
Label protocol |
250 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, 200 ng of RNA from each of the 19 tumor samples were combined and labeled in batches of 500 ng 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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|
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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) |
GSE49888 |
Ovarian Cancer: 19 ovarian tumors of diverse histologic type vs. pool of all 19 tumors. |
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