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Sample GSM1208946 Query DataSets for GSM1208946
Status Public on Jan 17, 2014
Title Serous ovarian tumor C008 vs. 19 OVCA tumor pool
Sample type RNA
 
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).
 
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).
 
 
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)
GSE49888 Ovarian Cancer: 19 ovarian tumors of diverse histologic type vs. pool of all 19 tumors.

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

Data table
ID_REF VALUE
12 1.385395824
13 0.776203642
14 -0.146840701
15 -0.027788717
16 1.331796521
17 0.692420711
18 0.859542368
19 -0.016641223
20 0.595625559
21 0.797970087
22 -0.736413507
23 0.117225241
24 0.043557879
25 -1.193467967
26 0.562622019
27 -2.283425054
28 -1.413239796
29 0.042459653
30 0.307261443
31 0.344264216

Total number of rows: 43118

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM1208946_OVCA_C008_vs_OVCA_pool.txt.gz 15.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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