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Sample GSM714379 Query DataSets for GSM714379
Status Public on Apr 27, 2011
Title L90
Sample type genomic
 
Channel 1
Source name Ovarian cancer_formalin fixed, paraffin embedded
Organism Homo sapiens
Characteristics histology: clear cell
mutation: Mismtach repair
differentiation: 2
figo stage: I
age: 42
Treatment protocol Formalin fixed, paraffin embedded
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from formalin fixed, paraffin embedded tumor tissue according to protocols from the UCSF Waldman Laboratory, San Francisco, CA, USA (http://cc.ucsf.edu/people/waldman/Protocols/paraffin.html), with an additional purification step using Phase Lock Gel tubes (Eppendorf AG, Hamburg, Germany).
Label Cy3
Label protocol 2-8 μg tumor DNA and 2 µg reference DNA (Promega Corporation, Madison, WI, USA) were labeled with Cy3-dCTP and Cy5-dCTP, using BioPrime Array CGH Genomic Labeling System (Invitrogen Life Technologies, Carlsbad, CA, USA).
 
Channel 2
Source name Pooled male reference
Organism Homo sapiens
Characteristics gender: Male
Treatment protocol Formalin fixed, paraffin embedded
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from formalin fixed, paraffin embedded tumor tissue according to protocols from the UCSF Waldman Laboratory, San Francisco, CA, USA (http://cc.ucsf.edu/people/waldman/Protocols/paraffin.html), with an additional purification step using Phase Lock Gel tubes (Eppendorf AG, Hamburg, Germany).
Label Cy5
Label protocol 2-8 μg tumor DNA and 2 µg reference DNA (Promega Corporation, Madison, WI, USA) were labeled with Cy3-dCTP and Cy5-dCTP, using BioPrime Array CGH Genomic Labeling System (Invitrogen Life Technologies, Carlsbad, CA, USA).
 
 
Hybridization protocol Hybridizations were conducted using the MAUI® Hybridization System (BioMicro systems Inc, Salt Lake City, UT, USA).
Scan protocol The slides were scanned in an Agilent Microarray Scanner (Agilent Technologies).
Description 90_cy3
Data processing TIFF images were analysed using the GenePixTM Pro. 4.1 software (Axon Instruments Inc., Foster City, CA, USA) and quantified data matrices were uploaded in the web based BioArray Software Environment software (BASE) (Saal et al., 2002). Positive and nonsaturated spots were background corrected using the median background intensities for each channel and log2 ratios were calculated from the background corrected intensities. Data were filtered for flagged features and spots below signal to noise ratio 3 for both channels were eliminated. Data was normalized using an implementation of a population based LOWESS algorithm (Staaf et al., 2007).
 
Submission date Apr 25, 2011
Last update date Apr 27, 2011
Contact name Katarina Bartuma
E-mail(s) katarina.bartuma@med.lu.se
Organization name department of Oncology
Street address Barn garan 2b
City Lund
ZIP/Postal code 221 85
Country Sweden
 
Platform ID GPL4723
Series (1)
GSE28850 Genomic profiling of hereditary epithelial ovarian cancer using tiling resolution array CGH

Data table header descriptions
ID_REF
VALUE lowess normalized log2 ratio (tumor/reference)

Data table
ID_REF VALUE
16114 -0.10010470034636157
21614 -0.19242275674272413
25469 -0.20501639265754212
28383 -0.17722770857981301
8727 -0.02291354941582281
6520 -0.4618109227121722
10890 -0.3083921375150869
14569 -0.2954319682098731
27130 -0.3093563153199394
11653 0.2626463416088734
1416 0.040368767290664465
19111 1.328762610245339
19756 1.1627607221434957
33609 0.8801826087497863
25591 1.0212624284690972
32861 0.8296990474430095
24132 0.6811871309250069
32882
28512 0.15920064809175807
22670 0.9163342830764067

Total number of rows: 31919

Table truncated, full table size 781 Kbytes.




Supplementary file Size Download File type/resource
GSM714379.gpr.gz 2.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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