Sample Set Annotation Tool: Upper airway gene expression is an effective surrogate biomarker for Th2-driven inflammation in the lower airway

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Molecular profiling studies in asthma cohorts have identified a Th2-driven asthma subtype, characterized by elevated lower airway expression of POSTN, CLCA1 and SERPINB2. To assess upper airway gene expression as a potential biomarker for lower airway Th2 inflammation, the study assayed upper airway (nasal) and lower airway (bronchial) epithelial gene expression, serum total IgE, blood eosinophils and serum periostin in a cohort of 54 allergic asthmatics and 30 matched healthy controls.

Hypothesis

Upper airway gene expression as a potential biomarker for lower airway Th2 inflammation

Experimental Design

Upper airway (nasal) and lower airway (bronchial) epithelial brushings obtained from a cohort of 54 allergic asthmatics and 30 matched healthy controls were profiled by gene expression by microarray. Subjects were assayed for gene expression, serum total IgE, blood eosinophils and serum periostin.

Experimental Variables

Allergic asthma

Controls

30 healthy controls

Methods

Additional Information

Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. Log2 RMA signal intensity.

Expected Samples:

138 Samples Loaded: 138

Species

Human (Homo sapiens)

Sample Source

Bronchial biopsies , Nasal epithelial tissue

Disease

Asthma

Treatment Protocol

Growth Protocol

Extraction Protocol

Total RNA was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol.

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	Age	tissue	group	severity	disease
GSM1026433	54	Nasal	Asthma_Moderate_N	Moderate	Asthma
GSM1026434	44	Nasal	Asthma_Mild_N	Mild	Asthma
GSM1026435	42	Nasal	Healthy_Control_N	Healthy	Control
GSM1026436	54	Nasal	Healthy_Control_N	Healthy	Control
GSM1026437	32	Nasal	Asthma_Severe_N	Severe	Asthma

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File
GSE41861_v1.csv Sample Set Spreadsheet
GSE41861_v1.csv Sample Set Spreadsheet

Samples Viewer / Editor

All fields are editable except the "Sample ID" column. To edit a cell, click within the cell. To edit a "date" cell, click on the calendar icon. To cancel an edit, press the ESC key.

Sample ID	Age	Tissue	Group	Severity	Disease	Sample	Sex
GSM1026433	54	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-003	M
GSM1026434	44	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-004	M
GSM1026435	42	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-009	M
GSM1026436	54	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-010	M
GSM1026437	32	Nasal	Asthma_Severe_N	Severe	Asthma	NS_AA-012	F
GSM1026438	30	Nasal	Asthma_Severe_N	Severe	Asthma	NS_AA-014	F
GSM1026439	33	Nasal	Asthma_Severe_N	Severe	Asthma	NS_AA-018	F
GSM1026440	32	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-019	F
GSM1026441	31	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-020	F
GSM1026442	38	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-021	M
GSM1026443	22	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-022	F
GSM1026444	24	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-023	F
GSM1026445	46	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-024	M
GSM1026446	23	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-025	F
GSM1026447	34	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-026	M
GSM1026448	23	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-028	F
GSM1026449	36	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-029	F
GSM1026450	39	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-031	F
GSM1026451	29	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-032	M
GSM1026452	24	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-034	M
GSM1026453	26	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-035	F
GSM1026454	40	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-037	M
GSM1026455	42	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-038	M
GSM1026456	66	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-039	F
GSM1026457	52	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-040	F
GSM1026458	26	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-041	M
GSM1026459	36	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-042	F
GSM1026460	35	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-043	F
GSM1026461	24	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-044	M
GSM1026462	27	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-045	F
GSM1026463	31	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-046	F
GSM1026464	40	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-047	M
GSM1026465	22	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-051	F
GSM1026466	33	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-052	M
GSM1026467	30	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-054	F
GSM1026468	31	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-055	F
GSM1026469	28	Nasal	Asthma_Severe_N	Severe	Asthma	NS_AA-056	F
GSM1026470	30	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-057	M
GSM1026471	20	Nasal	Asthma_Severe_N	Severe	Asthma	NS_AA-058	F
GSM1026472	53	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-059	M
GSM1026473	37	Nasal	Healthy_Control_N	Healthy	Control	NS_AA-064	F
GSM1026474	30	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-065	M
GSM1026475	25	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-074	M
GSM1026476	33	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-077	M
GSM1026477	28	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-082	M
GSM1026478	49	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-083	M
GSM1026479	44	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-084	M
GSM1026480	21	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-086	F
GSM1026481	47	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-087	F
GSM1026482	43	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-088	M
GSM1026483	19	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-089	F
GSM1026484	58	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-090	M
GSM1026485	38	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-092	F
GSM1026486	27	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-093	M
GSM1026487	36	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-094	F
GSM1026488	42	Nasal	Asthma_Moderate_N	Moderate	Asthma	NS_AA-095	M
GSM1026489	19	Nasal	Asthma_Mild_N	Mild	Asthma	NS_AA-096	M
GSM1026490	44	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-002	M
GSM1026491	54	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-003	M
GSM1026492	44	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-004	M
GSM1026493	43	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-005	M
GSM1026494	28	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-006	F
GSM1026495	21	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-007	F
GSM1026496	37	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-008	M
GSM1026497	42	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-009	M
GSM1026498	54	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-010	M
GSM1026499	32	Bronchial	Asthma_Severe_Bronchial	Severe	Asthma	LAE_AA-012	F
GSM1026500	22	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-013	F
GSM1026501	30	Bronchial	Asthma_Severe_Bronchial	Severe	Asthma	LAE_AA-014	F
GSM1026502	28	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-015	M
GSM1026503	34	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-016	F
GSM1026504	48	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-017	M
GSM1026505	33	Bronchial	Asthma_Severe_Bronchial	Severe	Asthma	LAE_AA-018	F
GSM1026506	32	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-019	F
GSM1026507	31	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-020	F
GSM1026508	38	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-021	M
GSM1026509	22	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-022	F
GSM1026510	24	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-023	F
GSM1026511	46	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-024	M
GSM1026512	23	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-025	F
GSM1026513	34	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-026	M
GSM1026514	23	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-028	F
GSM1026515	36	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-029	F
GSM1026516	49	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-030	M
GSM1026517	39	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-031	F
GSM1026518	29	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-032	M
GSM1026519	24	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-034	M
GSM1026520	26	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-035	F
GSM1026521	40	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-037	M
GSM1026522	42	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-038	M
GSM1026523	66	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-039	F
GSM1026524	52	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-040	F
GSM1026525	26	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-041	M
GSM1026526	36	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-042	F
GSM1026527	35	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-043	F
GSM1026528	24	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-044	M
GSM1026529	27	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-045	F
GSM1026530	31	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-046	F
GSM1026531	40	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-047	M
GSM1026532	37	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-048	F
GSM1026533	24	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-049	M
GSM1026534	22	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-051	F
GSM1026535	33	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-052	M
GSM1026536	43	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-053	F
GSM1026537	30	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-054	F
GSM1026538	31	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-055	F
GSM1026539	28	Bronchial	Asthma_Severe_Bronchial	Severe	Asthma	LAE_AA-056	F
GSM1026540	30	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-057	M
GSM1026541	20	Bronchial	Asthma_Severe_Bronchial	Severe	Asthma	LAE_AA-058	F
GSM1026542	53	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-059	M
GSM1026543	30	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-062	F
GSM1026544	54	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-063	F
GSM1026545	37	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-064	F
GSM1026546	30	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-065	M
GSM1026547	23	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-066	F
GSM1026548	19	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-067	M
GSM1026549	64	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-068	F
GSM1026550	51	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-069	F
GSM1026551	54	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-070	F
GSM1026552	29	Bronchial	Healthy_Control_Bronchial	Healthy	Control	LAE_AA-073	M
GSM1026553	25	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-074	M
GSM1026554	22	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-076	M
GSM1026555	33	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-077	M
GSM1026556	19	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-079	M
GSM1026557	34	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-080	M
GSM1026558	28	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-082	M
GSM1026559	46	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-085	F
GSM1026560	21	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-086	F
GSM1026561	47	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-087	F
GSM1026562	43	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-088	M
GSM1026563	58	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-090	M
GSM1026564	40	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-091	F
GSM1026565	38	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-092	F
GSM1026566	27	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-093	M
GSM1026567	36	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-094	F
GSM1026568	42	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-095	M
GSM1026569	19	Bronchial	Asthma_Mild_Bronchial	Mild	Asthma	LAE_AA-096	M
GSM1026570	28	Bronchial	Asthma_Moderate_Bronchial	Moderate	Asthma	LAE_AA-097	F

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