|
| Status |
Public on Jun 14, 2010 |
| Title |
UC_0179_1_Hv3_35k_h1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Urinary bladder tumor UC_0179_1
|
| Organism |
Homo sapiens |
| Characteristics |
sample histology: Upper urinary tract urothelial carcinoma
tumor stage: Ta
tumor grade: G3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue homogenization and RNA recovery using TRIzol reagent (Invitrogen), followed by purification of total RNA using RNeasy kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Labeling of 5 micrograms of sample RNA was performed using the Pronto Plus System (Promega)
|
| |
|
| Channel 2 |
| Source name |
Stratagene Universal Human Reference
|
| Organism |
Homo sapiens |
| Characteristics |
reference: RNA pooled from ten human cell lines
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue homogenization and RNA recovery using TRIzol reagent (Invitrogen), followed by purification of total RNA using RNeasy kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
Labeling of 5 micrograms of sample RNA was performed using the Pronto Plus System (Promega)
|
| |
|
| |
| Hybridization protocol |
Samples were dissolved in 42 microliter Universal Hybridization Solution (Corning) and hybridizations were carried out in a CMT-Hybridization Chamber (Corning) for 18 h at 42°C. Pre-hybridization of slides and post-hybridization washes were performed using the Pronto Plus System (Promega)
|
| 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)
|
| Description |
UC_0179_1_Hv3_35k_h1
This is one of two samples that were hybridized to both 27k and 35k platforms. They were only used for merging of the two expression datasets.
|
| 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 intensities <15 were removed. Data was normalized using pin-based LOWESS algorithm.
|
| |
|
| Submission date |
Jan 15, 2010 |
| Last update date |
Jan 19, 2010 |
| 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 |
GPL5186 |
| Series (1) |
| GSE19915 |
Subtype classification, grading, and outcome prediction of urothelial carcinomas by combined mRNA profiling and aCGH |
|
