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Skin biopsies (92 EM and 87 control biopsies) were analysed using quantitative real-time PCR for detection of B. burgdorferi DNA.
Tumour biopsies were analysed using gene expression profiling with Affymetrix GeneChip® microarrays.
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Total RNA extracted from malignant (n = 75), normal (n = 15), and fibroadenoma (n = 10) breast tissue biopsies was analysed using RQ-PCR targeting NIS, RARα, RARβ, ERα, PI3K, THRα and THRβ.
A subset of pre-ischaemic left ventricular biopsies was analysed using mass spectrometry-based metabolomics.
For biopsy specimens, comet slides were analysed using a single-blind approach in that patient details were not made available until comet analysis was completed.
Pairwise comparison of expression in biopsies and operative samples was analysed using a nonparametric paired-samples test (Wilcoxon signed-ranks test).
Concordance of CA IX expression between preoperative biopsies and operative samples was analysed using non-parametric paired-samples test (Wilcoxon signed ranks test or McNemar test).
Biopsies from chronic wounds were analysed using classical culture methods by plating on selective agar for the detection of S. aureus and P. aeruginosa.
The prevalence of H. pylori infection in this cohort of patients undergoing upper GI endoscopy was 39%, and this is comparable to the findings of a similar endoscopy-based study from the same hospital in which multiple gastric biopsies were analysed for H. pylori using PCR (Balaratnam et al, 2001).
Levels of mitochondrial point mutations in snap frozen synovial biopsies were analysed in a blinded fashion using Mitochondrial Random Mutation Capture assay as described previously [ 22].
Biopsies were analysed under light and electron microscopy and appearance systematically quantified by expert renal pathologists blinded to group allocation and time of biopsy.
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