Single cell RNAseq coupled with TCR repertoire analysis of thymocytes in thymus autonomy and turnover

Wild type thymi were transplanted into wild recipients (turnover) or Rag2-/-gc-/- mice (autonomy) and, after 28 days of transplant, thymocytes (double negative 3 and 4, immature CD8 single positive and CD4 CD8 double positive) were sorted and single cell RNAseq and TCR repertoire analysis performed Single cell analysis of the transcriptome and VDJ rearrangements of thymocytes in autonomy or turnover conditions.