IEL, LPL or peripheral blood lymphocytes (1–5 × 106) were each diluted in 200 µl PBS containing 0·6 mM/ml Proteinase K (Sigma-Aldrich) and 200 µl lysis buffer AL (QIAamp DNA Blood Mini kit, Qiagen, Hilden, Germany), incubated for 10 min at 56°C and then stored at room temperature in lysis buffer AL until further use. IEL, LPL or intestinal mucosal biopsies (2 × 106) were also incubated in RNAlater

ACP-196 (Ambion, Austin, TX, USA) at 4°C overnight and then stored at −80°C. Peripheral blood and mucosal lymphocytes (1 × 106) in a volume of 30 µl were incubated at 4°C for 20 min with a cocktail of the following antibodies: anti-CD4-APC, anti-CD3-peridinin chlorophyll (PerCP), anti-CD62L-phycoerythrin (PE) and anti-CD45RA-fluorescein isothiocyanate (FITC) (BD multi-test for naive CD4+ T cells; BD Biosciences, San Jose, CA, USA). For analysis of extrathymic maturation of T lymphocytes in the intestinal mucosa, 1 × 106 LPL in a volume of 30 µl were stained with the following mouse anti-human antibodies CD2-PECy5, CD3-Pacific-blue (clone: UCHT1), CD5-APC (clone: L1712), CD7-FITC, CD16-PE and CD19-PE (all from BD Biosciences). Isotype controls were mouse immunoglobulin (Ig)G1-PE, mouse IgG2a-FITC, mouse IgG1-PECy5, mouse IgG2a-APC (clone: G155-178) and mouse

IgG1-Pacific blue (clone: MOPC-21) (all from BD Biosciences). For analysis of the check details frequency of proliferating T lymphocytes in peripheral blood the cells were prestained with anti-CD3 Pacific-blue, permeabilized and fixed with 100 µl fixation and permeabilization buffer (Nordic BioSite, Täby, Sweden), incubated at 4°C overnight and stained with Ki-67-PE or isotype control IgG1κ (Ki-67 PE-conjugated reagent set; BD Biosciences Pharmingen) in 50 µl permeabilization buffer (Nordic BioSite).

Flow cytometry was performed by acquisition of at least 20 000 lymphocytes, based on forward- and side light-scatter characteristics, on a BD LSR II (BD Biosciences) and subsequent analysis was performed using FlowJo software (Tree Star Inc., San Carlo, CA, USA). Genomic DNA from peripheral blood or mucosal lymphocytes was purified by the QIAamp DNA Blood Mini kit (Qiagen) according to the manufacturer’s instructions. Prior to the PCR, the DNA concentrations in all samples were determined by ultraviolet spectrophotometry diglyceride at 260 and 280 nm wavelengths and adjusted to a concentration of 30 ng/µl. The amount of TRECs relative to the amount of the reference DNA sequence, originating from the glyceraldehyde-3-phosphate dehydrogenase (GAPDH), was determined by quantitative real-time PCR (LightCycler 1·2; Roche Diagnostics GmbH, Roche Applied Science, Mannheim, Germany), using specific primers and the fluorescent dye SybrGreen I for detection of the specific products. The PCR primers were purchased from Scandinavian Gene Synthesis AB (Köping, Sweden).