Extended Data Fig. 9: scTCR-Seq and genetic barcoding experiments reveal derivation of IGRP-specific pancreatic T cells from pLN TCF1hi population.
From: An autoimmune stem-like CD8 T cell population drives type 1 diabetes
a, Alluvial plots tracking the size of non shared (yellow) and shared clonotypes in pLN TCF1hi, pLN TCF1lo, and pancreas (PA) populations from n = 21 mice. Each non-yellow stratum represents a clonotype that is found across multiple populations. b, Number of pancreatic T cells from individual mice that contain clonotypes that were either found in pLN TCF1hi (red) or not found in pLN TCF1hi (orange) population. Each row represents one individual mouse. c, Number of clonotypes across all mice that are shared with at least one other population (blue) or non-shared (yellow) in pLN TCF1hi and pLN TCF1lo populations. d, Fraction of clonotypes in pLN TCF1hi and pLN TCF1lo populations from individual mice that are shared with at least one other population (blue) or non-shared (yellow). Each row represents one mouse. e, Bar plot (top) and Venn diagram (bottom) displaying the different populations from which a given clonotype was recovered. The numbers are based on all clonotypes from all mice for which paired information from pLN and pancreas was available. f, Top, pie charts represent number of cells in each population containing clonotypes from pLN TCF1hi that are shared with at least one other population (n = 127 clonotypes, identified in Extended Data Fig. 9c). Bottom, median number of cells per clonotype in each population split by shared and non shared clonotypes. Each dot represents the cell count from a single mouse. For box plots, center indicates median, lower and upper hinges indicate 25th and 75th percentiles, respectively, and whiskers extend up to 1.5xIQR (inter-quartile range) from the smallest/highest values; points shown individually fall outside that range. Notches extend 1.58xIQR/sqrt(n), roughly indicating 95% confidence interval for comparing medians. g, Cells from one example shared clonotype are shown within the coordinates of the scRNA-seq based diffusion map. Individual cells are colored according to their cluster membership. h, Left, Alluvial plots from genetic barcoding experiment show barcodes detected in pLN TCF1hi 8.3 and pancreatic 8.3 for n = 2 mice; Right, Venn diagrams show numbers of barcodes detected in pLN TCF1hi 8.3 (to achieve 99% barcode coverage) and expanded in pancreas (>1% of barcodes detected).
