Thymic iNKT cells in Prkd2/3 mice (scRNA/TCR-seq, scATAC-seq)

We have conducted single cell-RNA, -TCR, -ATAC sequencing (10x Genomics) to investigate a difference of gene expression, TCR repertoir and chromatin accesibility of thymic iNKT cells from wild-type and CD4-Cre-mediated T cell-specific Prkd2/3 doubly deficirnt (Prkd2/3ΔCD4) mice. Results demonstrate that Prkd2/3 are required for iNKT cell development and formaion of proper iNKT cell subtypes. Thymus was taken from wild-type and Prkd2/3ΔCD4 mice. Thymic iNKT cells were enriched by CD1d-tetramer using MACS magnetic separators followed by purification by a cell sorter. Cells were applied to scRNA/TCR-seq analysis. For scATAC-seq analysis, nuclei were ioslated from purified cells according to manufacture's protocol (10x Genomics).