Fig. 3

Count-based analysis of TCR alpha and beta chain variable gene transcripts across the filtered 71 mice T-cell samples. a Heatmap of percentage of nucleotide BLAST-mapped TRBV genes mapping to individual TRBV genes (x-axis) across 71 mouse T-cell samples (y-axis). Increasing shades of blue denote increased percentage of all TRBV-mapping reads mapping to a particular TRBV gene. b Heatmap of percentage of nucleotide BLAST-mapped TRAV genes mapping to individual TRAV genes (x-axis) across 71 mouse T-cell samples (y-axis). Increasing shades of red denote increased percentage of all TRAV-mapping reads mapping to a particular TRAV gene. c Log-log plot of total reads that nucleotide BLAST-mapped to TCR variable regions. The x-axis measures the logarithm of the count of total reads mapping to any TRBV gene for a single sample and the y-axis measures the logarithm of the count of total reads mapping to any TRAV gene. Each colored point represents an individual mouse T-cell samples with read points denoting GFP negative T-cells and blue points denoting GFP positive T-cells. The lines at x = 2.3 and y = 1.9 represent cutoffs for which samples were selected for further analysis based upon their expression of TCR transcripts (bottom 10th percentile cutoff). The 59 samples in the upper right quadrant of the figure underwent further targeted assembly. d Heatmap of paired TCR alpha and beta chain expression with x-axis representing chosen TCR beta chain V usage and the y-axis representing TCR alpha chain V usage. Color scale ranged from white for no particular (TRBV, TRAV) usage to dark orange for two samples observing the same (TRBV, TRAV) usage