The slide was washed with Gene Expression

wash buffer 1 (Agilent Technologies, Wilmington, DE, USA) for 1 min at RT and Gene Expression wash buffer 2 (Agilent Technologies, Wilmington, DE, USA) for 1 min at 37 °C. 10% Triton X-102 was added to both washing solutions to final concentration of 0.005%. The fluorescent signals were detected at 5 or 10 μm resolution using a GenePix Autoloader 4200AL laser scanning system with green laser for Cy3 dye (ex 543 nm/em 570 nm) and blue laser for 6-FAM (ex 488 nm/em 495 nm). The laser power was set at 100% and the photomultiplier (PMT) tube was LGK-974 cell line adjusted according to the intesity of the signal. GenePix program version 6.1 was used to quantitate the signal from each spot. The microarray data PXD101 in vivo is included in Additional files Torin 2 datasheet 4 5 6. Microarray data analysis The microarray data were managed using R-software [39] and Bioconductor package marray[43]. The microarray raw signals were processed as described previously [41]. Briefly, after local background subtraction, the control channel values were multiplied by the ratio of medians of probe channel and control channel. Next, negative values were removed

and probe channel signals were adjusted as L i ‘ = L ilog(L i/C i), where L i is the raw probe channel signal value at feature i and Ci is the adjusted control channel signal value at feature i. Further normalisation in sensitivity tests with Arrayit microarrays was executed by dividing all signals by a control ligation probe signal.

Alignment of probe sequences to template sequences was done in R using local pairwise alignment functions from package Biostrings[40]. The used nucleotide substitution matrix had match score of 1 and mismatch score of −2. The microarray data have been deposited to ArrayExpress with accession numbers E-MEXP-3539 (sensitivity Methane monooxygenase tests), E-MEXP-3541 (reactor samples), E-MEXP-3538 (specificity tests). Quantitative PCR experiments A TaqMan probe (5′-AGGAACATGTGGTTTA-3′) was designed to hybridise to the same position as the corresponding microarray ligation probe (A123). The probe harbored a 5′ VIC® reporter dye, a 3′ non-fluorescent quencher and a MGB™ (minor groove binder). The PCR reaction mixture for amplification of the TaqMan probe target region contained 1X Genotyping Master Mix (Applied Biosystems, Foster City, CA, USA), 900 nM forward primer (5′-GAAAGCGATAAGTTATCCACCTGGG-3′), 900 nM reverse primer (5′-TTCGAGCCCGGGTAAGGTTCC-3′), 250 nM TaqMan probe and approximately 50 ng of environmental DNA in a final volume of 20 μl. The PCR program consisted of activation at 95 °C for 10 min and 40 cycles of denaturation at 95 °C for 30s and annealing/extension at 60 °C for 1 min. Each reaction had three replicates in the assay plate.