Table 1.

Sequence reads and CDR3 for different subsets of T cells

SubsetCell countEffective read* Total CDR3Unique CDR3
TCRαTCRβ
aanaaana
Tr6.30 × 107 206,087179,35434,80438,77322,90623,654
Th11.84 × 108 174,046150,12229,47132,51819,64420,061
Th21.94 × 107 105,56791,36914,03815,3016,2506,447
Tc1.69 × 108 221,832200,41216,65418,2149,3109,735
Tn+t9.52 × 107 213,054191,12122,72824,65213,94714,373
Ta8.89 × 106 187,494167,7279,05210,0843,8734,129
Tm1.45 × 107 168,301146,76216,30218,04915,08115,536
pan T3.77 × 107 283,241251,66537,85742,04526,98127,960
pan T 80,24671,76515,63816,62210,30810,483
pan T§ 30,57927,2637,7948,1305,3345,416
Total1,670,4471,477,560137,751169,977106,903113,290
Public 1,3111,222203210916938
  • Tr, T regulatory cell (CD4+CD25+); Th1, T helper cell 1 (CD4+CD25−CD294−); Th2, T helper cell 2 (CD4+CD25−CD294+); Tc, T cytotoxic cell (CD8+); Tn+t, naïve and transitional T cell (CD45RA+); Ta, activated T cell (CD45-RO-CD69+); Tm, memory T cell (CD45RA-RO+); aa, amino acids; na, nucleic acids.

  • *An effective read is a read that can be mapped with both V and J germline segments.

  • A unique CDR3 sequence is a nonredundant fragment of amino acids (aa) or nucleic acids (na), which is in a stop-codon-free reading frame containing both translated conserved motifs ( SI Text ).

  • ‡,§pan T samples were processed along with pan B cells and T cell counts for these two samples were not recorded.

  • Public sequence data set was compiled by combining relevant cDNA sequences in both the GenBank and the IMGT database. Reported here are those passed through the analysis pipeline.