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Sample GSM805953 Query DataSets for GSM805953
Status Public on Jun 18, 2012
Title Bladder tumor UC_0053_1_aCGH_h2
Sample type genomic
 
Channel 1
Source name bladder tumor UC_0053_1
Organism Homo sapiens
Characteristics histology: Urothelial carcinoma
tumor stage: T1
tumor grade: G3
tissue: bladder cancer tumor
Treatment protocol Urothelial carcinoma samples were collected by cold-cup biopsy from the exophytic part of the bladder tumor of patients undergoing transurethral resecrtions at hospitals within the southern healthcare region of Sweden
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using Trizol reagent (Invitrogen) and further purified using the Wizard kit (Promega)
Label cy3
Label protocol 1.5 microgram sample and reference genomic DNA was labeled with Cy5-dCTP or with Cy3-dCTP (Amersham Biosciences) using random primer labeling (Bioprime array CGH genomic Labeling module, Invitrogen), and purified using filter-based spin columns (Cyscribe GFX Purification kit, Amersham Biosciences).
 
Channel 2
Source name Reference female DNA
Organism Homo sapiens
Characteristics sample type: Reference female DNA
Treatment protocol Urothelial carcinoma samples were collected by cold-cup biopsy from the exophytic part of the bladder tumor of patients undergoing transurethral resecrtions at hospitals within the southern healthcare region of Sweden
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using Trizol reagent (Invitrogen) and further purified using the Wizard kit (Promega)
Label cy5
Label protocol 1.5 microgram sample and reference genomic DNA was labeled with Cy5-dCTP or with Cy3-dCTP (Amersham Biosciences) using random primer labeling (Bioprime array CGH genomic Labeling module, Invitrogen), and purified using filter-based spin columns (Cyscribe GFX Purification kit, Amersham Biosciences).
 
 
Hybridization protocol Differentially labeled DNA was pooled, mixed with 100 microgram Human Cot-1 DNA (Invitrogen), and lyophilized prior to resuspension in 55 microliter hybridization solution (50% formamide, 10% dextran sulfate, 2x SSC, 2% SDS, 10 mg/ml yeast tRNA). Probes were heated at 70°C for 15 minutes and at 37°C for 30 minutes before hybridization to micro arrays for 48-72 hours at 37°C. Prior to hybridization, micro arrays were UV-cross linked at 500 mJ/cm2 and pretreated using the Universal Micro array Hybridization Kit (Corning, Acton, MA) according to the manufacturer's instructions. The slides were washed in 2 x SSC, 0.1% SDS for 15 min, followed by 2 x SSC, 50% formamide (pH 7.0) for 15 min at 45°C, 2 x SSC, 0.1% SDS for 30 min at 45°C, and 0.2 x SSC for 15 min at room temperature.
Scan protocol Fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies). Image analysis on scanned arrays was performed with GenePix 4.0 (Axon Instruments)
Data processing Data was processed in the BioArray Software Environment (BASE). For each channel, the Mean FG - Median BG intensity value was used. Features flagged bad/missing or saturated during image analysis were removed. Poorly measured features with Ch1 or Ch2 signal to noise ratio (SNR) <5 were removed. Data was normalized using the popLowess method (Staaf, et al, BMC Genomics, 2007, 8:382)
 
Submission date Sep 30, 2011
Last update date Jun 18, 2012
Contact name David Lindgren
E-mail(s) david.lindgren@med.lu.se
Organization name Lund University
Department Dept of Laboratory Medicine
Lab Translational Cancer Research
Street address Building 404 A3, Scheelevägen 2, Medicon Village
City Lund
ZIP/Postal code SE-223 81
Country Sweden
 
Platform ID GPL4723
Series (2)
GSE32535 Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma (genomic)
GSE32549 Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy3/Cy5) representing test/reference

Data table
ID_REF VALUE
1 0.432
2 -0.245
3 0.178
4 -0.102
5 0.069
6 -0.222
7 -0.168
8 -0.065
9 -0.387
10 0.089
11 0.492
12 0.014
13 -0.172
14 -0.236
15 -0.248
16 0.082
17 -0.172
18 0.8
19 -0.112
20 0.069

Total number of rows: 31941

Table truncated, full table size 370 Kbytes.




Supplementary file Size Download File type/resource
GSM805953_3043_01.aCGH.2.gpr.gz 2.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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