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Sample GSM1556527 Query DataSets for GSM1556527
Status Public on Dec 02, 2014
Title 0003830049|KE Contact Eczema
Sample type RNA
 
Channel 1
Source name Common skin reference
Organism Homo sapiens
Characteristics tissue: whole skin biopsy
sample type: skin biopsies from pool of 160 patients with skin disorders and healthy donors
Extracted molecule total RNA
Extraction protocol Isolation of total RNA from skin excision biopsies was performed using TriReagent (Sigma, St Louis, MO) and the NucleoSpin 96 RNA Kit (Macherey & Nagel, Dueren, Germany). RNA was quantified by photometrical measurement, and the integrity was checked using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Label Cy3
Label protocol Samples were labeled with FluoroLinkk Cy3/Cy5-dCTP (100 µg total RNA per sample, Amersham Pharmacia Biotech, Freiburg, Germany).
 
Channel 2
Source name skin disease
Organism Homo sapiens
Characteristics tissue: whole skin biopsy
sample type: Contact Eczema
Extracted molecule total RNA
Extraction protocol Isolation of total RNA from skin excision biopsies was performed using TriReagent (Sigma, St Louis, MO) and the NucleoSpin 96 RNA Kit (Macherey & Nagel, Dueren, Germany). RNA was quantified by photometrical measurement, and the integrity was checked using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Label Cy5
Label protocol Samples were labeled with FluoroLinkk Cy3/Cy5-dCTP (100 µg total RNA per sample, Amersham Pharmacia Biotech, Freiburg, Germany).
 
 
Hybridization protocol The fluorescently labeled samples were hybridized overnight to topic-defined PIQOR (TM) Skin 2.0 Microarrays Human Antisense using the GeneTAC hybridisation station (Genomics Solutions).
Scan protocol Image capture and signal quantification of hybridized PIQOR ™Skin 2.0 microarrays were done with the ScanArrayLite4000 Microarray Scanner (Packard-Biosciences) and ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA).
Data processing Signals were analysed with the PIQOR Analyzer software (Miltenyi Biotec, Bergisch Gladbach, Germany). The PIQOR Analyzer allows automated data processing of the raw data text files (_1b = Cy3 channel and _2b = Cy5 channel) derived from the ImaGene software. This includes background subtraction to obtain the net signal intensity, data normalization, and calculation of the Cy5/Cy3 ratios. Subsequently, the mean of the ratios of the four corresponding spots representing the same cDNA was computed. The ratios were normalized using the LOWESS method. As an additional quality filtering step, only genes were taken into account for the calculation of the Cy5/Cy3 ratio that have at least in one channel a signal intensity that was at least 2-fold higher than the mean background
 
Submission date Dec 01, 2014
Last update date Dec 02, 2014
Contact name Joerg Wenzel
E-mail(s) joerg.wenzel@ukb.uni-bonn.de
Organization name University of Bonn
Department Dermatology
Street address Sigmund Freud Str 25
City Bonn
ZIP/Postal code 53121
Country Germany
 
Platform ID GPL19471
Series (1)
GSE63741 Gene Expression Analyses of Homo sapiens Inflammatory Skin Diseases

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3) representing disease/common skin reference

Data table
ID_REF VALUE
3 0.9151
5 0.5111
16 0.3229
18 1.6634
20 -0.0171
33 0.1519
35 -0.4435
37 0.1197
39 0.2608
43 -0.412
47 -0.2642
49 0.3439
55 -1.0978
57 -0.4121
59 0.0686
61 0.2122
67 0.0744
71 0.1385
73 0.5002
81 -0.2221

Total number of rows: 1542

Table truncated, full table size 19 Kbytes.




Supplementary file Size Download File type/resource
GSM1556527_000383_049_1b.txt.gz 1.4 Mb (ftp)(http) TXT
GSM1556527_000383_049_2b.txt.gz 1.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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