Sample Set Annotation Tool: Expression data for human epithelium from subjects with atopic dermatitis, psoriasis and nonatopic controls-GSE26952

Study Design
Assay
Sample Info
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Info
Samples
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Analysis

Purpose

The expression and function of tight junction genes, in particular claudin-1, was studied in order to further understanding of the biology underlying atopic dermatitis.

Hypothesis

Experimental Design

Gene expression profiling was performed on total RNA from nonlesional epidermal samples from 5 subjects with atopic dermatitis, 4 subjects withpsoriasis, and 5 nonatopic controls using the Illumina Sentrix HumanRef-8 Expression BeadChip. There were duplicate (technical replicate) arrays run for 2 of the nonatopic control samples (the normalized transformed expression values of replicate pairs were averaged before performing data analysis, also, for each probe, the combined value for replicate pairs of Detection Pvalues was taken to be their minimum - so a Present call for one of the replicate pair of expression values results in a Present call for the combined (average) expression value).Details of the design and the results found are given in the paper associated with this GEO Series.

Experimental Variables

Controls

Methods

Additional Information

De Benedetto A, Rafaels NM, McGirt LY, Ivanov AI et al. Tight junction defects in patients with atopic dermatitis. J Allergy Clin Immunol 2011 Mar;127(3):773-86.e1-7. PMID: 21163515

Expected Samples:

16 Samples Loaded: 16

Species

Human (Homo sapiens)

Sample Source

Epithelium

Disease

Psoriasis

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Sample ID	Age	!Sample_title	Sex	race	rast (radioallergosorbent test)
GSM663510	20s	Nonlesional Epithelium Atopic Dermatitis rep1	m	Native American	detects IgE that reacts specifically with suspected or known allergens: positive
GSM663511	50s	Nonlesional Epithelium Atopic Dermatitis rep2	m	Caucasian	detects IgE that reacts specifically with suspected or known allergens: positive
GSM663512	20s	Nonlesional Epithelium Atopic Dermatitis rep3	f	African American	detects IgE that reacts specifically with suspected or known allergens: positive
GSM663513	40s	Nonlesional Epithelium Atopic Dermatitis rep4	f	Caucasian	detects IgE that reacts specifically with suspected or known allergens: positive
GSM663514	30s	Nonlesional Epithelium Atopic Dermatitis rep5	f	Caucasian	detects IgE that reacts specifically with suspected or known allergens: positive

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Sample ID	Age	!Sample Title	Sex	Race	Rast (radioallergosorbent test)	Ige (kiu/l)	Eosinophil level (cells/ml)	Ar or asthma	Easi/pasi	Disease group
GSM663510	20s	Nonlesional Epithelium Atopic Dermatitis rep1	m	Native American	detects IgE that reacts specifically with suspected or known allergens: positive	normal (0-48.5 kIU/L): 4136	normal (120-300 cells/ml): 990	YES, subject has history of AR (allergic rhinitis), asthma or both: YES	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 11.6	Atopic Dermatitis
GSM663511	50s	Nonlesional Epithelium Atopic Dermatitis rep2	m	Caucasian	detects IgE that reacts specifically with suspected or known allergens: positive	normal (0-48.5 kIU/L): 710	normal (120-300 cells/ml): 510	YES, subject has history of AR (allergic rhinitis), asthma or both: YES	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 34.6	Atopic Dermatitis
GSM663512	20s	Nonlesional Epithelium Atopic Dermatitis rep3	f	African American	detects IgE that reacts specifically with suspected or known allergens: positive	normal (0-48.5 kIU/L): 2578	normal (120-300 cells/ml): 290	YES, subject has history of AR (allergic rhinitis), asthma or both: YES	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 15.2	Atopic Dermatitis
GSM663513	40s	Nonlesional Epithelium Atopic Dermatitis rep4	f	Caucasian	detects IgE that reacts specifically with suspected or known allergens: positive	normal (0-48.5 kIU/L): 319	normal (120-300 cells/ml): 430	YES, subject has history of AR (allergic rhinitis), asthma or both: YES	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 11.3	Atopic Dermatitis
GSM663514	30s	Nonlesional Epithelium Atopic Dermatitis rep5	f	Caucasian	detects IgE that reacts specifically with suspected or known allergens: positive	normal (0-48.5 kIU/L): 36	normal (120-300 cells/ml): 100	YES, subject has history of AR (allergic rhinitis), asthma or both: YES	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 4.5	Atopic Dermatitis
GSM663515	30s	Nonlesional Epithelium Psoriasis rep1	m	African American	detects IgE that reacts specifically with suspected or known allergens: positive	normal (0-48.5 kIU/L): 224	normal (120-300 cells/ml): 360	YES, subject has history of AR (allergic rhinitis), asthma or both: no	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 34	Psoriasis
GSM663516	20s	Nonlesional Epithelium Psoriasis rep2	m	Caucasian	detects IgE that reacts specifically with suspected or known allergens: negative	normal (0-48.5 kIU/L): 31.2	normal (120-300 cells/ml): 110	YES, subject has history of AR (allergic rhinitis), asthma or both: no	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 3	Psoriasis
GSM663517	30s	Nonlesional Epithelium Psoriasis rep3	f	Caucasian	detects IgE that reacts specifically with suspected or known allergens: positive	normal (0-48.5 kIU/L): 49.3	normal (120-300 cells/ml): 10	YES, subject has history of AR (allergic rhinitis), asthma or both: YES	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 9.1	Psoriasis
GSM663518	30s	Nonlesional Epithelium Psoriasis rep4	f	Caucasian	detects IgE that reacts specifically with suspected or known allergens: negative	normal (0-48.5 kIU/L): 18.2	normal (120-300 cells/ml): 140	YES, subject has history of AR (allergic rhinitis), asthma or both: no	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 6.6	Psoriasis
GSM663519	20s	Nonlesional Epithelium Nonatopic Control rep1	m	Caucasian	detects IgE that reacts specifically with suspected or known allergens: negative	normal (0-48.5 kIU/L): 70.8	normal (120-300 cells/ml): 90	YES, subject has history of AR (allergic rhinitis), asthma or both: no	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 0	Nonatopic Control
GSM663520	20s	Nonlesional Epithelium Nonatopic Control rep2a	f	Caucasian	detects IgE that reacts specifically with suspected or known allergens: negative	normal (0-48.5 kIU/L): 2.5	normal (120-300 cells/ml): 50	YES, subject has history of AR (allergic rhinitis), asthma or both: YES	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 0	Nonatopic Control
GSM663521	20s	Nonlesional Epithelium Nonatopic Control rep2b	f	Caucasian	detects IgE that reacts specifically with suspected or known allergens: negative	normal (0-48.5 kIU/L): 2.5	normal (120-300 cells/ml): 50	YES, subject has history of AR (allergic rhinitis), asthma or both: YES	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 0	Nonatopic Control
GSM663522	40s	Nonlesional Epithelium Nonatopic Control rep3	m	Caucasian	detects IgE that reacts specifically with suspected or known allergens: negative	normal (0-48.5 kIU/L): 2	normal (120-300 cells/ml): 140	YES, subject has history of AR (allergic rhinitis), asthma or both: no	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 0	Nonatopic Control
GSM663523	40s	Nonlesional Epithelium Nonatopic Control rep4a	m	African American	detects IgE that reacts specifically with suspected or known allergens: negative	normal (0-48.5 kIU/L): 2.9	normal (120-300 cells/ml): 160	YES, subject has history of AR (allergic rhinitis), asthma or both: no	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 0	Nonatopic Control
GSM663524	40s	Nonlesional Epithelium Nonatopic Control rep4b	m	African American	detects IgE that reacts specifically with suspected or known allergens: negative	normal (0-48.5 kIU/L): 2.9	normal (120-300 cells/ml): 160	YES, subject has history of AR (allergic rhinitis), asthma or both: no	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 0	Nonatopic Control
GSM663525	20s	Nonlesional Epithelium Nonatopic Control rep5	m	Caucasian	detects IgE that reacts specifically with suspected or known allergens: positive	normal (0-48.5 kIU/L): 34.7	normal (120-300 cells/ml): 130	YES, subject has history of AR (allergic rhinitis), asthma or both: no	disease severity score, range (0-72). Arbitrarily, we assigned 0 to Controls. EASI is used for Atopic Dermatitis and PASI for Psoriasis: 0	Nonatopic Control

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