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Additional file 3: Figure S3. Spectratype analysis of patient PBMCs without prior short term culture. TCR repertoire analysis including 34 TCRα and 24 TCRβ families. Numbers indicate CDR3 sequencing data gained in direct sequencing approaches (see Table 3). Peak numbers marked in grey harbor CMV-specific sequences.

Additional file 5: Figure S5. Peptide-responsive clones at IM3 all displayed an CD45RA+ effector memory TEMRA phenotype. One representative example (clone #54) is shown in (a). In contrast, clones obtained from control cultures without peptide stimulation expressed a CD45RAneg effector memory phenotype, data by clone #6 are shown in (b).

Additional file 2: Figure S2. Activation markers expressed by vaccine-reactive T cell clones at IM3. T cells responding to vaccine peptide stimulation with IFN-Îł+ production were analyzed for their expression of the activation markers CD25, CD69 and HLA-DR by flow cytometry.

Additional file 1: Figure S1. Work flow of immune monitoring techniques.

Additional file 4: Figure S4. Clonality analysis of 21 control cultures (without peptide stimulation) at IM3 was performed by flow cytometry. All control clones were found to express all the same TCRVβ chain (BV 6-2), confirming molecular data, indicating a common, high-frequency progenitor in peripheral blood. (a) shows representative flow cytometry data of clone #6. Individual TCRβ antibody staining are achieved by combining 3 TCR Vβ-specific reagents in a single test using only two colors for mab conjugation: one TCR Vβ antibody is conjugated to FITC, another one to PE, and the third to both FITC and PE. In this way, the third Vβ-stained population shows up in the diagonal of the upper right quadrant in a FL1/FL2 histogram. The CDR3 sequence of the analyzed clone (b) is identical to a TCR sequence specific for mycolic acid [41].