Sample Set Annotation Tool: Profiling of naïve and memory Tregs-GSE76598

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Changes in Treg function are difficult to quantify due to the lack of Treg-exclusive markers in humans and the complexity of functional experiments. We sorted naive and memory human Tregs and conventional T cells, and identified genes that identify human Tregs regardless of their state of activation. We developed this Treg signature using Affymetrix human genome U133A 2.0 microarrays.To generate Tregs and Tconvs in multiple states of activation, naïve (CD4+CD25hiCD45RA+) and memory (CD4+CD25hiCD45RA-) Tregs, and naïve (CD4+CD25-CD45RA+) and memory (CD4+CD25-CD45RA-) Tconvs were sorted from blood of 7 healthy adults and RNA was isolated ex vivo or after stimulation for 40h, promoting activation-induced FOXP3 in Tconvs. The gene-expression profile of the eight cell subsets was analyzed.

Hypothesis

Experimental Design

7 adult healthy control samples were sorted into 4 subsets: naïve (CD4+CD25hiCD45RA+) and memory (CD4+CD25hiCD45RA-) Tregs, and naïve (CD4+CD25-CD45RA+) and memory (CD4+CD25-CD45RA-) Tconvs. These were used for RNA ex vivo and after 40h stimulation with anti-CD3/CD28 beads to induce an activation phenotype.

Experimental Variables

Controls

Methods

Additional Information

Pesenacker AM, Wang AY, Singh A, Gillies J et al. A Regulatory T-Cell Gene Signature Is a Specific and Sensitive Biomarker to Identify Children With New-Onset Type 1 Diabetes. Diabetes 2016 Apr;65(4):1031-9. PMID: 26786322

Expected Samples:

52 Samples Loaded: 52

Species

Human (Homo sapiens)

Sample Source

Regulatory T Cells

Disease

Healthy

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	!Sample_title	individual	treatment	cell subset	Grouping
GSM2028716	MLS010	donor 1	unstimulated	naiveTreg	Non_naiveTreg
GSM2028717	MLS011	donor 1	unstimulated	memoryTconv	Non_mTcov
GSM2028718	MLS014x	donor 1	stimulated	naiveTreg	Sti_naiveTreg
GSM2028719	MLS015	donor 7	stimulated	memoryTconv	Sti_mTconv
GSM2028720	MLS016	donor 1	stimulated	naiveTconv	Sti_naiveTconv

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File
sampleset4000036_sampleannotations (1).csv Sample Set Spreadsheet

Samples Viewer / Editor

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Sample ID	!Sample Title	Individual	Treatment	Cell subset	Grouping
GSM2028716	MLS010	donor 1	unstimulated	naiveTreg	Non_naiveTreg
GSM2028717	MLS011	donor 1	unstimulated	memoryTconv	Non_mTcov
GSM2028718	MLS014x	donor 1	stimulated	naiveTreg	Sti_naiveTreg
GSM2028719	MLS015	donor 7	stimulated	memoryTconv	Sti_mTconv
GSM2028720	MLS016	donor 1	stimulated	naiveTconv	Sti_naiveTconv
GSM2028721	MLS025	donor 1	unstimulated	memoryTreg	Non_mTreg
GSM2028722	MLS026	donor 2	unstimulated	naiveTreg	Non_naiveTreg
GSM2028723	MLS027	donor 2	unstimulated	memoryTconv	Non_mTcov
GSM2028724	MLS028	donor 1	unstimulated	naiveTconv	Non_naiveTconv
GSM2028725	MLS029	donor 1	stimulated	memoryTreg	Sti_mTreg
GSM2028726	MLS030	donor 2	stimulated	naiveTreg	Sti_naiveTreg
GSM2028727	MLS031	donor 1	stimulated	memoryTconv	Sti_mTconv
GSM2028728	MLS032	donor 2	stimulated	naiveTconv	Sti_naiveTconv
GSM2028729	MLS033	donor 2	unstimulated	memoryTreg	Non_mTreg
GSM2028730	MLS034	donor 3	unstimulated	naiveTreg	Non_naiveTreg
GSM2028731	MLS035	donor 3	unstimulated	memoryTconv	Non_mTcov
GSM2028732	MLS036	donor 2	unstimulated	naiveTconv	Non_naiveTconv
GSM2028733	MLS037	donor 2	stimulated	memoryTreg	Sti_mTreg
GSM2028734	MLS038	donor 3	stimulated	naiveTreg	Sti_naiveTreg
GSM2028735	MLS039	donor 2	stimulated	memoryTconv	Sti_mTconv
GSM2028736	MLS040	donor 3	stimulated	naiveTconv	Sti_naiveTconv
GSM2028737	MLS041	donor 3	unstimulated	memoryTreg	Non_mTreg
GSM2028738	MLS042	donor 4	unstimulated	naiveTreg	Non_naiveTreg
GSM2028739	MLS044	donor 3	unstimulated	naiveTconv	Non_naiveTconv
GSM2028740	MLS045	donor 3	stimulated	memoryTreg	Sti_mTreg
GSM2028741	MLS046	donor 4	stimulated	naiveTreg	Sti_naiveTreg
GSM2028742	MLS047	donor 3	stimulated	memoryTconv	Sti_mTconv
GSM2028743	MLS048	donor 4	stimulated	naiveTconv	Sti_naiveTconv
GSM2028744	MLS065	donor 4	unstimulated	memoryTreg	Non_mTreg
GSM2028745	MLS066x	donor 5	unstimulated	naiveTreg	Non_naiveTreg
GSM2028746	MLS067x	donor 4	unstimulated	memoryTconv	Non_mTcov
GSM2028747	MLS068	donor 4	unstimulated	naiveTconv	Non_naiveTconv
GSM2028748	MLS069x	donor 4	stimulated	memoryTreg	Sti_mTreg
GSM2028749	MLS070	donor 5	stimulated	naiveTreg	Sti_naiveTreg
GSM2028750	MLS071	donor 4	stimulated	memoryTconv	Sti_mTconv
GSM2028751	MLS072	donor 5	stimulated	naiveTconv	Sti_naiveTconv
GSM2028752	MLS073x	donor 5	unstimulated	memoryTreg	Non_mTreg
GSM2028753	MLS074x	donor 6	unstimulated	naiveTreg	Non_naiveTreg
GSM2028754	MLS075	donor 5	unstimulated	memoryTconv	Non_mTcov
GSM2028755	MLS076	donor 5	unstimulated	naiveTconv	Non_naiveTconv
GSM2028756	MLS077x	donor 5	stimulated	memoryTreg	Sti_mTreg
GSM2028757	MLS078	donor 6	stimulated	naiveTreg	Sti_naiveTreg
GSM2028758	MLS079	donor 5	stimulated	memoryTconv	Sti_mTconv
GSM2028759	MLS080	donor 6	stimulated	naiveTconv	Sti_naiveTconv
GSM2028760	MLS081x	donor 6	unstimulated	memoryTreg	Non_mTreg
GSM2028761	MLS082	donor 7	unstimulated	naiveTreg	Non_naiveTreg
GSM2028762	MLS083	donor 6	unstimulated	memoryTconv	Non_mTcov
GSM2028763	MLS084x	donor 6	unstimulated	naiveTconv	Non_naiveTconv
GSM2028764	MLS085	donor 6	stimulated	memoryTreg	Sti_mTreg
GSM2028765	MLS086	donor 7	stimulated	naiveTreg	Sti_naiveTreg
GSM2028766	MLS087	donor 6	stimulated	memoryTconv	Sti_mTconv
GSM2028767	MLS088x	donor 7	stimulated	naiveTconv	Sti_naiveTconv

Group Sets View in Gene Expression Browser

Name
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Culture conditions	Default	View
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Module Analysis

Group Set
All Samples
Culture conditions

SIDRA