Fig. S1. Toll-like receptor (TLR)-2, TLR-4 and hypoxanthine–guanine phosphoribosyltransferase (HPRT) mRNA expression by isolated and disaggregated intestinal crypt epithelial cells obtained from histologically normal (control) small intestine (lane 1), inflamed small bowel Crohn's disease (lane 2), histologically normal (control) large intestine (lane 3), inflamed colonic Crohn's disease (lane 4) and inflamed large intestinal mucosal samples affected by ulcerative colitis (lane 5). Following reverse transcription, extracted RNA was used for polymerase chain reaction (PCR) using specific primer pairs and controls included omission of reverse transcriptase (lane 6) and lack of cDNA template (lane 7). The figure is representative of experiments undertaken using crypt epithelial cells isolated from ≥ 5 specimens for each group identified in lanes 1–5. L = DNA size markers.

Table S1. Details of patients studied. TNFα = tumour necrosis factor-α. *P < 0·05; **P < 0·01 versus healthy controls.

Table S2. Relative quantitative expression of Toll-like receptor (TLR)-2 and TLR-4 mRNA transcripts in isolated and disaggregated colonic and small intestinal crypt epithelial cells obtained from histologically normal control mucosal samples and those affected by active ulcerative colitis (UC), Crohn's colitis and ileal Crohn's disease. Extracted RNA was used for real-time reverse transcription–polymerase chain reaction (RT–PCR) and data for UC and Crohn's disease are presented as ‘fold change’ in expression of transcripts compared to mean expression in the control group in which the crypt epithelial cells were obtained from histologically normal colonic and small intestinal mucosal samples. IQR = interquartile range.

Table S3. Quantitative surface Toll-like receptor (TLR)-2 and TLR-4 protein expression by colonic crypt epithelial cells. Isolated and disaggregated crypt epithelial cells were obtained from mucosal samples affected by active Crohn's colitis, active ulcerative colitis or from histologically normal control colonic tissue. The cells were labelled with anti-BerEP4-fluorescein isothiocyanate (FITC) antibody and either anti-TLR-2 allophycocyanin (APC), anti-TLR-4-APC or isotype control monoclonal antibodies and analysed by flow cytometry. Surface TLR-2 and TLR-4 protein-associated median fluorescence intensity was determined in BerEP4-positive (gated) epithelial cells. IQR = interquartile range.

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