Single-cell RNAseq (10x Genomics) analysis of mouse splenic CD4+ T cells in WT and deltaFoxp3 mice and in WT/deltaFoxp3 bone marrow chimeras

Single-cell RNAseq (10x Genomics) analysis of mouse splenic CD4+ T cells in WT and deltaFoxp3 mice and in WT/deltaFoxp3 bone marrow chimeras. Mouse CD4+T cells in 21-day-old male WT and deltaFoxp3 mice were isolated from spleen by flow cytometry as DAPI-TCRbeta+CD4+ cells for 10x Genomics Single Cell 3' Reagent Kit (V2 chemistry, one sample per channel). For bone marrow chimera experiment: 7 week-old CD45.2-recipient mice were irradiated with 1000 Rad, reconstituted with 4 million CD3-depleted bone marrow cells: 50% CD45.1 x Foxp3-IRES-GFP (WT, 21d-old male) and 50% Foxp3DeltaEGFPiCre/RFP x ROSA-YFP x CD45.1/2 (scurfy, 21d-old male). 10 weeks later, spleen were harvested and tagged using a different Hashtags fo each mouse. deltaFoxp3 CD4+ T cells were sorted as DAPI-TCRb+CD4+CD45.1+CD45.2+. WT CD4+ T cells were sorted as DAPI-TCRb+CD4+CD45.1+CD45.2-. Control WT DAP-TCRb+CD4+GFP+ Treg cells and GFP- Tconvs cells were also tagged and sorted. Samples with different hastags were pooled before single cell encapsulation using 10x Genomics Single Cell 3' Reagent Kit (V3 chemistry). Mouse CD4+T cells in 21-day-old male WT and deltaFoxp3 mice were isolated from spleen by flow cytometry as DAPI-TCRbeta+CD4+ cells for 10x Genomics Single Cell 3' Reagent Kit (V2 chemistry, one sample per channel). For bone marrow chimera experiment: 7 week-old CD45.2-recipient mice were irradiated with 1000 Rad, reconstituted with 4 million CD3-depleted bone marrow cells: 50% CD45.1 x Foxp3-IRES-GFP (WT, 21d-old male) and 50% Foxp3DeltaEGFPiCre/RFP x ROSA-YFP x CD45.1/2 (scurfy, 21d-old male). 10 weeks later, spleen were harvested and tagged using a different Hashtags fo each mouse. deltaFoxp3 CD4+ T cells were sorted as DAPI-TCRb+CD4+CD45.1+CD45.2+. WT CD4+ T cells were sorted as DAPI-TCRb+CD4+CD45.1+CD45.2-. Control WT DAPI-TCRb+CD4+GFP+ Treg cells and GFP- Tconvs cells were also tagged and sorted. Samples with different hastags were pooled before single cell encapsulation using 10x Genomics Single Cell 3' Reagent Kit (V3 chemistry).