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 Overall design: Single cell analysis of the transcriptome and VDJ rearrangements of thymocytes in autonomy or turnover conditions.