Sample Set Annotation Tool: Transcriptome profiling of 1) nasal polyp-derived human IL17RB positive and negative T-helper cells and 2) T-helper cells from normal nasal mucosa and matched peripheral blood

Study Design
Assay
Sample Info
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Analysis

Purpose

To investigate the role of the IL-25/IL-33 axis in local mucosal T cell responses in CRSwNP.

Hypothesis

TH2 cells characterize nasal polyps with a default TH17 signature in nasal

Experimental Design

Polyp tissue and blood were obtained from patients undergoing nasal polypectomy. Control nasal biopsies and blood were obtained from healthy volunteers. Tissue was cultured in a short-term explant model. T cell surface phenotype/intracellular cytokines were assessed by flow cytometry. Cells were then activated with PMA/Ionomycin for 4hrs or left in a resting state.

Experimental Variables

PMA/Ionomycinm and expression of IL17RB

Controls

3 healthy donors

Methods

Polyp tissue and blood were obtained from patients undergoing nasal polypectomy. Control nasal biopsies and blood were obtained from healthy volunteers. Tissue was cultured in a short-term explant model. T cell surface phenotype/intracellular cytokines were assessed by flow cytometry. TCR V? analysis was performed with the immunoSEQ assay. Microarrays were performed for gene expression analysis.

Additional Information

The data correspond to the merge of GSE70898 and GSE70900 and further details can be found on the GEO website at:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70898

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70900

Expected Samples:

24 Samples Loaded: 24

Species

Human (Homo sapiens)

Sample Source

CD4 T cells

Disease

Rhinitis

Treatment Protocol

T-helper cells were sorted based upon expression of CD4 in normal control and expression of IL17RB in patients using flow cytometric sorting. Cells were then activated with PMA/Ionomycin for 4hrs or left in a resting state.

Growth Protocol

Extraction Protocol

RNA was isolated from cell pellets using the miRNeasy mini kit and RNeasy MinElute cleanup kit (Qiagen, Manchester, UK) according to the manufacturer’s instructions.

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	!Sample Title	tissue	group	Cell type	Disease state
GSM1821439	IL17RB- Resting_rep1	Nasal polyp tissue	P_Nasal_neg_Rest	T-helper cells	chronic rhinosinusitis
GSM1821440	IL17RB- Activated_rep1	Nasal polyp tissue	P_Nasal_neg_Act	T-helper cells	chronic rhinosinusitis
GSM1821441	IL17RB+ Resting_rep1	Nasal polyp tissue	P_Nasal_pos_Rest	T-helper cells	chronic rhinosinusitis
GSM1821442	IL17RB+ Activated_rep1	Nasal polyp tissue	P_Nasal_pos_Act	T-helper cells	chronic rhinosinusitis
GSM1821443	IL17RB- Resting_rep2	Nasal polyp tissue	P_Nasal_neg_Rest	T-helper cells	chronic rhinosinusitis

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File
GSE70900_70898.csv Sample Set Spreadsheet

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Sample ID	!Sample Title	Tissue	Group	Cell type	Disease state	Cell subtype
GSM1821439	IL17RB- Resting_rep1	Nasal polyp tissue	P_Nasal_neg_Rest	T-helper cells	chronic rhinosinusitis	IL17RB- Resting
GSM1821440	IL17RB- Activated_rep1	Nasal polyp tissue	P_Nasal_neg_Act	T-helper cells	chronic rhinosinusitis	IL17RB- Activated
GSM1821441	IL17RB+ Resting_rep1	Nasal polyp tissue	P_Nasal_pos_Rest	T-helper cells	chronic rhinosinusitis	IL17RB+ Resting
GSM1821442	IL17RB+ Activated_rep1	Nasal polyp tissue	P_Nasal_pos_Act	T-helper cells	chronic rhinosinusitis	IL17RB+ Activated
GSM1821443	IL17RB- Resting_rep2	Nasal polyp tissue	P_Nasal_neg_Rest	T-helper cells	chronic rhinosinusitis	IL17RB- Resting
GSM1821444	IL17RB- Activated_rep2	Nasal polyp tissue	P_Nasal_neg_Act	T-helper cells	chronic rhinosinusitis	IL17RB- Activated
GSM1821445	IL17RB+ Resting_rep2	Nasal polyp tissue	P_Nasal_pos_Rest	T-helper cells	chronic rhinosinusitis	IL17RB+ Resting
GSM1821446	IL17RB+ Activated_rep2	Nasal polyp tissue	P_Nasal_pos_Act	T-helper cells	chronic rhinosinusitis	IL17RB+ Activated
GSM1821447	IL17RB- Resting_rep3	Nasal polyp tissue	P_Nasal_neg_Rest	T-helper cells	chronic rhinosinusitis	IL17RB- Resting
GSM1821448	IL17RB- Activated_rep3	Nasal polyp tissue	P_Nasal_neg_Act	T-helper cells	chronic rhinosinusitis	IL17RB- Activated
GSM1821449	IL17RB+ Resting_rep3	Nasal polyp tissue	P_Nasal_pos_Rest	T-helper cells	chronic rhinosinusitis	IL17RB+ Resting
GSM1821450	IL17RB+ Activated_rep3	Nasal polyp tissue	P_Nasal_pos_Act	T-helper cells	chronic rhinosinusitis	IL17RB+ Activated
GSM1821463	Blood resting_rep1	peripheral blood	C_Blood_Rest	T-helper cells	healthy control	resting
GSM1821464	Blood resting_rep2	peripheral blood	C_Blood_Rest	T-helper cells	healthy control	resting
GSM1821465	Blood resting_rep3	peripheral blood	C_Blood_Rest	T-helper cells	healthy control	resting
GSM1821466	Blood activated_rep1	peripheral blood	C_Blood_Act	T-helper cells	healthy control	activated
GSM1821467	Blood activated_rep2	peripheral blood	C_Blood_Act	T-helper cells	healthy control	activated
GSM1821468	Blood activated_rep3	peripheral blood	C_Blood_Act	T-helper cells	healthy control	activated
GSM1821469	Normal nasal resting_rep1	nasal mucosa	C_Nasal_Rest	T-helper cells	healthy control	resting
GSM1821470	Normal nasal resting_rep2	nasal mucosa	C_Nasal_Rest	T-helper cells	healthy control	resting
GSM1821471	Normal nasal resting_rep3	nasal mucosa	C_Nasal_Rest	T-helper cells	healthy control	resting
GSM1821472	Normal nasal activated_rep1	nasal mucosa	C_Nasal_Act	T-helper cells	healthy control	activated
GSM1821473	Normal nasal activated_rep2	nasal mucosa	C_Nasal_Act	T-helper cells	healthy control	activated
GSM1821474	Normal nasal activated_rep3	nasal mucosa	C_Nasal_Act	T-helper cells	healthy control	activated

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SIDRA