Dataset: Genomic definition of multiple ex vivo Treg sub-phenotypes

Regulatory T (Treg) cells that express the FoxP3 transcription factor are essential for lymphoid homeostasis and immune tolerance to...

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Regulatory T (Treg) cells that express the FoxP3 transcription factor are essential for lymphoid homeostasis and immune tolerance to self. Other non-immunological functions of Treg cells, such as controlling metabolic function in adipose tissue, are also emerging. Treg cells originate primarily in the thymus, but can also be elicited from conventional T cells by in vivo exposure to low-dose antigen or homeostatic expansion, or by activation in the presence of TGFβ in vitro. Treg cells are characterized by a distinct transcriptional signature controlled in part, but not solely, by FoxP3. For a better perspective on transcriptional control in Treg cells, we compared gene expression profiles of a broad panel of Treg cells from various origins or anatomical locations. Treg cells generated by different means form different sub-phenotypes identifiable by particular combinations of transcripts, none of which fully encompass the entire Treg signature. Molecules involved in Treg effector function, chemokine receptors, and the transcription factors that control them are differentially represented in these subphenotypes. Treg cells from the gut proved dissimilar to cells elicited by exposure to TGFβ, but instead they resembled a CD103+Klrg1+ subphenotype preferentially generated in response to lymphopenia. All gene expression profiles were obtained from highly purified T cell populations sorted by flow cytometry. To reduce variability, cells from multiple mice were pooled for sorting, and replicates or triplicates were generated for all groups. RNA from 1-5 x 104 cells was amplified, labeled, and hybridized to Affymetrix M430v2 microarrays. Raw data were preprocessed with the RMA algorithm in GenePattern, and averaged expression values were used for analysis.

Species:: mouse
Samples:: 23
Source:: E-GEOD-20366
Updated:: Dec.12, 2014
Registered:: Nov.11, 2014

Factors: (via ArrayExpress)

Sample	NUMBER OF MICE PER CHIP	CELL TYPE	GENOTYPE/VARIATION
GSM510238	4-6	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+ T cells were sorted from the small intestinal lamina propria (cell isolation from Sun et al J. Exp. Med. 2007).	C57BL/6-Foxp3/GFP
GSM510238	4-6	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+ T cells were sorted from the small intestinal lamina propria (cell isolation from Sun et al J. Exp. Med. 2007).	C57BL/6-Foxp3/GFP
GSM510240	4-6	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP- T cells were sorted from the small intestinal lamina propria (cell isolation from Sun et al J. Exp. Med. 2007).	C57BL/6-Foxp3/GFP
GSM510240	4-6	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP- T cells were sorted from the small intestinal lamina propria (cell isolation from Sun et al J. Exp. Med. 2007).	C57BL/6-Foxp3/GFP
GSM510242	2-3	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+ T cells were sorted from the spleen and lymph nodes 14 days after IV transfer into NOD RAG-/- hosts.	BDC2.5/NOD/Foxp3-GFP- CD4+ T cells were transferred into NOD RAG-/- mice
GSM510242	2-3	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+ T cells were sorted from the spleen and lymph nodes 14 days after IV transfer into NOD RAG-/- hosts.	BDC2.5/NOD/Foxp3-GFP- CD4+ T cells were transferred into NOD RAG-/- mice
GSM510242	2-3	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+ T cells were sorted from the spleen and lymph nodes 14 days after IV transfer into NOD RAG-/- hosts.	BDC2.5/NOD/Foxp3-GFP- CD4+ T cells were transferred into NOD RAG-/- mice
GSM510245	5-10	CD3+, B220-, CD8a-, CD11b/c-, CD4+CD25+ T cells were sorted from the spleen and lymph nodes 3 wks after transfer into Balb/c hosts.	HA6.5/Thy1.2/RAG-/-/Balb/c CD4+CD25- T cells were transferred into Balb/c mice and treated with a singel injection of DEC-HAPeptide (50ng/mouse)
GSM510245	5-10	CD3+, B220-, CD8a-, CD11b/c-, CD4+CD25+ T cells were sorted from the spleen and lymph nodes 3 wks after transfer into Balb/c hosts.	HA6.5/Thy1.2/RAG-/-/Balb/c CD4+CD25- T cells were transferred into Balb/c mice and treated with a singel injection of DEC-HAPeptide (50ng/mouse)
GSM510245	5-10	CD3+, B220-, CD8a-, CD11b/c-, CD4+CD25+ T cells were sorted from the spleen and lymph nodes 3 wks after transfer into Balb/c hosts.	HA6.5/Thy1.2/RAG-/-/Balb/c CD4+CD25- T cells were transferred into Balb/c mice and treated with a singel injection of DEC-HAPeptide (50ng/mouse)
GSM510248	4-6	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+CD103-Klrg1- T cells were sorted from the peripheral lymph nodes.	C57BL/6-Foxp3/GFP
GSM510248	4-6	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+CD103-Klrg1- T cells were sorted from the peripheral lymph nodes.	C57BL/6-Foxp3/GFP
GSM510250	4-6	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+CD103+Klrg1- T cells were sorted from the peripheral lymph nodes.	C57BL/6-Foxp3/GFP
GSM510250	4-6	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+CD103+Klrg1- T cells were sorted from the peripheral lymph nodes.	C57BL/6-Foxp3/GFP
GSM510252	4-6	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+CD103+Klrg1+ T cells were sorted from the peripheral lymph nodes.	C57BL/6-Foxp3/GFP
GSM510252	4-6	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP+CD103+Klrg1+ T cells were sorted from the peripheral lymph nodes.	C57BL/6-Foxp3/GFP
GSM5164	2-3	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP- T cells were sorted from the spleen and lymph nodes 14 days after IV transfer into NOD RAG-/- hosts	BDC2.5/NOD/Foxp3-GFP- CD4+ T cells were transferred into NOD RAG-/- mice
GSM5164	2-3	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP- T cells were sorted from the spleen and lymph nodes 14 days after IV transfer into NOD RAG-/- hosts	BDC2.5/NOD/Foxp3-GFP- CD4+ T cells were transferred into NOD RAG-/- mice
GSM5164	2-3	CD3+, B220-, CD8a-, CD11b/c-, CD4+Foxp3-GFP- T cells were sorted from the spleen and lymph nodes 14 days after IV transfer into NOD RAG-/- hosts	BDC2.5/NOD/Foxp3-GFP- CD4+ T cells were transferred into NOD RAG-/- mice
GSM516414	5-10	CD3+, B220-, CD8a-, CD11b/c-, CD4+CD25- T cells were sorted from the spleen and lymph nodes 3 wks after transfer into Balb/c hosts	HA6.5/Thy1.2/RAG-/-/Balb/c CD4+CD25- T cells were transferred into Balb/c mice and treated with a single injection of DEC-HAPeptide (50ng/mouse)
GSM516414	5-10	CD3+, B220-, CD8a-, CD11b/c-, CD4+CD25- T cells were sorted from the spleen and lymph nodes 3 wks after transfer into Balb/c hosts	HA6.5/Thy1.2/RAG-/-/Balb/c CD4+CD25- T cells were transferred into Balb/c mice and treated with a single injection of DEC-HAPeptide (50ng/mouse)
GSM516414	5-10	CD3+, B220-, CD8a-, CD11b/c-, CD4+CD25- T cells were sorted from the spleen and lymph nodes 3 wks after transfer into Balb/c hosts	HA6.5/Thy1.2/RAG-/-/Balb/c CD4+CD25- T cells were transferred into Balb/c mice and treated with a single injection of DEC-HAPeptide (50ng/mouse)
GSM516414	5-10	CD3+, B220-, CD8a-, CD11b/c-, CD4+CD25- T cells were sorted from the spleen and lymph nodes 3 wks after transfer into Balb/c hosts	HA6.5/Thy1.2/RAG-/-/Balb/c CD4+CD25- T cells were transferred into Balb/c mice and treated with a single injection of DEC-HAPeptide (50ng/mouse)