|
| Status |
Public on Oct 18, 2010 |
| Title |
No12-11PU |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Pigmented hair upper root sheaths
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pigmented hair upper root sheaths
|
| Biomaterial provider |
Department of Dermatology and Skin Science, University of British Columbia
|
| Treatment protocol |
Samples of human hair follicles were collected from scalp biopsies of normal individuals undergoing cosmetic procedures. Hair follicles were microdissected to remove the lower one third, including the hair bulb, leaving the root sheaths, including the bulge region.
|
| 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 |
1ug 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)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: multiple cell lines representing different human tissues
|
| Biomaterial provider |
Stratagene, Cedar Creek, TX
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The Universal Human Reference RNA is composed of total RNA isolated from cell lines representing different human tissues.
|
| 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). 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).
|
| Description |
All treated biologically replicated samples were hybridized with the same Universal Human Reference RNA (reference), which is composed of total RNA isolated from cell lines representing different human tissues for optimal broad gene coverage.
|
| Data processing |
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). Data were normalized using default global LOWESS normalization.
|
| |
|
| Submission date |
Sep 07, 2010 |
| Last update date |
Sep 15, 2010 |
| 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 (1) |
| GSE24009 |
Deficiency in nucleotide excision repair (NER) family gene activity, especially ERCC3, is associated with non-pigmented hair fiber growth |
|
