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Status |
Public on Jun 18, 2012 |
Title |
Bladder tumor UC_0053_1_aCGH_h2 |
Sample type |
genomic |
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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).
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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).
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|
|
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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)
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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 |
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