|
| Status |
Public on Dec 15, 2006 |
| Title |
Basal cell carcinoma_nodular_5 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
basal cell carcinoma_nodular
|
| Organism |
Homo sapiens |
| Characteristics |
basal cell carcinoma_nodular
|
| Biomaterial provider |
Department of Dermatology and Skin Science, University of British Columbia
|
| Treatment protocol |
sample was collected in the operating theater during Moh’s surgical excision
|
| Growth protocol |
sample was stored in an RNA stabilization reagent
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with an RNeasy Fibrous Tissue Midi Kit (Qiagen) according to the manufacturer's protocols.The quantity and quality of the RNAs was measured by electrophoresis using the Agilent 2100 bioanalyzer and RNA 6000 nano kit (Agilent Technologies, Palo Alto, CA).
|
| Label |
cy5
|
| Label protocol |
1 ug RNA were amplified using the SenseAmp plus kit (Genisphere Inc, Hatfield, PA). The calculated A 260/280 ratio was used to determine the appropriate amount of sense RNA for labeling. sense RNA from amplification was labeled with Cy5, with the 3DNA array detection 350 kit (Genisphere) and hybridized to cDNA microarrays.
|
| |
|
| Channel 2 |
| Source name |
universal human reference RNA (Stratagene, Cedar Creek, TX)
|
| Organism |
Homo sapiens |
| Characteristics |
The Universal Human Reference RNA is composed of total RNA isolated from cell lines representing different human tissues for optimal broad gene coverage.
|
| Biomaterial provider |
universal human reference RNA (Stratagene, Cedar Creek, TX)
|
| Treatment protocol |
universal human reference RNA (Stratagene, Cedar Creek, TX)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
universal human reference RNA (Stratagene, Cedar Creek, TX)
|
| Label |
cy3
|
| Label protocol |
Total 10ug RNA universal human reference RNA (Stratagene, Cedar Creek, TX) was labeled with Cy3 , with the 3DNA array detection 350 kit (Genisphere) and hybridized to cDNA microarrays.
|
| |
|
| |
| Hybridization protocol |
3DNA array detection 350 kit (Genisphere)
|
| Scan protocol |
The two fluorescent images (Cy3 and Cy5) were scanned separately using a Perkin Elmer ScanArray Express Scanner (PerkinElmer Life And Analytical Sciences, Inc., Wellesley, MA).
|
| Description |
All treated biologicaly replicated samples were hybridized with the same universal human reference RNA (reference).
|
| Data processing |
Arrays were scanned at excitation wave lengths of 532 and 635 nm to detect the Cy3 and Cy5 dyes, respectively. Image analysis and quantification were conducted with commercial software, (ImaGene 7.0 software: BioDiscovery Inc., El Segundo, CA, USA). After grid assignment, the adjusted intensity for each gene was calculated by subtracting the background. This value was used as the input for the Genespring 7.2 program (Silicon Genetics, Redwood City, CA, USA).
|
| |
|
| Submission date |
Nov 29, 2006 |
| Last update date |
Aug 25, 2008 |
| Contact name |
Kevin McElwee |
| E-mail(s) |
kmcelwee@interchange.ubc.ca
|
| Phone |
604-875-4747
|
| Organization name |
University of British Columbia
|
| Department |
Dermatology and Skin Science
|
| Lab |
Hair Research Laboratory
|
| Street address |
835 W. 10th Ave.
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V5Z 4E8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL3877 |
| Series (2) |
| GSE6520 |
Microarray analysis shows multiple signaling pathways are involved in basal cell carcinoma growth |
| GSE12542 |
Gene expression pattern similarity and differences between hair follicles and basal cell carcinomas |
|
