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Sample GSM147390 Query DataSets for GSM147390
Status Public on Dec 15, 2006
Title Normal control skin epithelium_1
Sample type RNA
 
Channel 1
Source name normal skin epithelium
Organism Homo sapiens
Characteristics normal skin epithelium
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

Data table header descriptions
ID_REF
PRE_VALUE The ratio of Cy5 (median signal minus median background) to Cy3 (median signal minus median background) which were taken from the Genespring software ,with a default global LOWESS normalization
CH1_SIG_MEDIAN channel1(cy5)sample median signal level
CH1_BKD_MEDIAN channel1(cy5)sample median background level
CH2_SIG_MEDIAN channel2(cy3)sample median signal level
CH2_BKD_MEDIAN channel2(cy3)sample median background level
VALUE log ratio(log2 of PRE_VALUE)

Data table
ID_REF PRE_VALUE CH1_SIG_MEDIAN CH1_BKD_MEDIAN CH2_SIG_MEDIAN CH2_BKD_MEDIAN VALUE
1.1.1.1 2.5031765 46417 243 13767 162.5 1.32376002
1.1.1.2 0.98699343 384 276 316.5 143 -0.018887614
1.1.1.3 0.4163371 1373.5 221 3000 162 -1.264175971
1.1.1.4 0.81445014 8183 203.5 8375.5 140.5 -0.296101714
1.1.1.5 0.28634477 183.5 176.5 178 114 -1.804174842
1.1.1.6 0.7219689 29826.5 230 38366 162.5 -0.469991403
1.1.1.7 0.67500144 225 191 220.5 139.5 -0.567037515
1.1.1.8 0.7329192 338 179 450.5 127 -0.448273936
1.1.1.9 4.5442924 10103 203 1992.5 139 2.184055667
1.1.1.10 0.68705505 235.5 172 272.5 123 -0.541502396
1.1.1.11 1.2793931 460.5 181 439 127 0.355459608
1.1.1.12 1.0412678 534 190 563.5 125 0.058341158
1.1.1.13 1.1913499 490 189 473.5 121 0.252597196
1.1.1.14 0.45303228 3514.5 200.5 6288 126 -1.142314244
1.1.1.15 0.55310863 825.5 197 1467 142 -0.854365243
1.1.1.16 0 172 180 152 120
1.1.1.17 0 144.5 172.5 125 121
1.1.1.18 0 175 179 175 133
1.1.1.19 0 197.5 215 109.5 95
1.1.1.20 0 181.5 177 140 107

Total number of rows: 23232

Table truncated, full table size 1138 Kbytes.




Supplementary file Size Download File type/resource
GSM147390_Cy3.txt.gz 2.9 Mb (ftp)(http) TXT
GSM147390_Cy5.txt.gz 2.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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