disease group: Atopic Dermatitis Sex: f age: 30s race: Caucasian easi/pasi: disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 4.5 ar or asthma: YES, subject has history of AR (allergic rhinitis), asthma or both: YES eosinophil level (cells/ml): normal (120-300 cells/ml): 100 ige (kiu/l): normal (0-48.5 kIU/L): 36 rast (radioallergosorbent test): detects IgE that reacts specifically with suspected or known allergens: positive s. aureus: Skin culture positive or negative for S. Aureus: neg
Extracted molecule
total RNA
Extraction protocol
Tissue samples were obtained and prepared as described in the Methods section of the paper cited in the overall design section of this GEO submission. Total RNA was extracted from epidermis by using the QIAshredder spin column and RNeasy RNA isolation kits (Qiagen, Hilden, Germany). The quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Total RNA was extracted from epidermis by using the QIAshredder spin column and RNeasy RNA isolation kits (Qiagen, Hilden, Germany). The quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Label
biotin
Label protocol
Biotin-labeled, complementary RNA (cRNA) was prepared from total RNA according to the chip manufacturer’s protocol (Illumina, San Diego, CA).
Hybridization protocol
cRNA was hybridized to Illumina Sentrix HumanRef-8 Expression BeadChips, and signal was detected with streptavidin-Cy3, using the standard Illumina hybridization protocol.
Scan protocol
All signal intensity quantification was performed using an Illumina BeadStation 500GX Genetic Analysis Systems scanner, using the standard Illumina scanning protocol.
Description
Atopic Dermatitis biological replicate 5
Data processing
A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina BeadStudio software with standard settings and no background correction. Two types of processed data were used for analysis: 1. Data was Z-transformed based on probes which were Present for at least one sample (the Illumina Detection Pvalue was < 0.01). Specifically, for each sample, define m to be the mean of the expression values for that sample taken over all probes present in at least 1 sample, and define s to be the corresponding standard deviation. Then for all the probes on the array, for that sample the Z-transformed expression value corresponding to an expression value e is (e-m)/s. 2. For use in calculating correlations of gene expression levels with the values of clinical variables; the expression values for all the probes for each sample were scaled to have median 256 and then log (base 2) transformed. For the data matrices, the ID_REF is the Illumina probe identifier, and the Detection Pval is the Illumina call for whether the measured expression level is Present (above background). Detection Pvalues near 0 indicate Present. In our analysis we considered expression values with a Detection Pvalue below 0.01 to be Present. Z-transformed data (item 1) provided as a supplementary file on GSE26952. Data median scaled (to median = 256) and then log base 2 transformed (item 2) included in Sample table.
