Figure 2.

(A,B) The abundance of high frequency CDR3s across repertoires of ovalbumin (OVA) or complete Freund’s adjuvant (CFA) mice. The 100 most abundant CDR3s from each OVA + CFA “early” repertoire (A) or CFA only “early” repertoire (B) were selected, and their abundance (shown as Log₂ counts/million) is shown in each OVA + CFA or CFA only immunized repertoire. Each column of the heat map represents one mouse repertoire. Each row of the heat map represents a distinct CDR3. Abundances below 2⁶ counts/million are in white. Pattern I indicates CDR3s which are abundant in both OVA + CFA and CFA only repertoires. Pattern II indicates CDR3s which are abundant in OVA + CFA repertoires. (C) The frequency distribution of the expansion index over all early immunized repertoires. The expansion index for each CDR3 is calculated as Log₂ (abundance in a specific repertoire/average abundance in all unimmunized repertoires). For those sequences present in immunized repertories but absent from all unimmunized repertories, the abundance in unimmunized mice was set to 1 in 10⁶ for calculation of expansion index. // shows that the column height is truncated. (D) The number of CDR3s in all early immunized repertoires with an expansion index greater than the threshold shown. The expansion index for each CDR3 is calculated as Log₂ (abundance in a specific repertoire/average abundance in all unimmunized repertoires). (E) The expansion index of all CDR3s with expansion index >6 in any OVA + CFA repertoire plotted for each OVA + CFA or CFA early immunized repertoires. Each column of the heat map represents one mouse repertoire. Each horizontal row of the heat map represents a distinct CDR3 with expansion index >6 in one or more OVA + CFA repertoires. Only those positions with an expansion index of >6 in that mouse are colored non-white. Pattern I indicates CDR3s which are abundant in both OVA + CFA and CFA only repertoires. Pattern II indicates CDR3s which are abundant in OVA + CFA repertoires.