Open Access Highly Accessed Methodology article

A short-oligonucleotide microarray that allows improved detection of gastrointestinal tract microbial communities

Carl R Harrington1*, Sacha Lucchini2, Karyn P Ridgway1, Udo Wegmann1, Tracy J Eaton1, Jay CD Hinton2, Michael J Gasson1 and Arjan Narbad1

Author Affiliations

1 Commensals and Microflora, Institute of Food Research, Norwich Research Park, Colney Lane, Norwich, Norfolk, NR4 7UA, UK

2 Pathogens: Molecular Microbiology, Institute of Food Research, Norwich Research Park, Colney Lane, Norwich, Norfolk, NR4 7UA, UK

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BMC Microbiology 2008, 8:195  doi:10.1186/1471-2180-8-195

Published: 11 November 2008

Additional files

Additional file 1:

Target organisms for 50-mer probes and actual tested microarray specificity using optimised hybridisation and washing conditions. Complete list of 50-mer probes used in this study with tested specificity results described for the optimum hybridisation and first washing temperatures of 65°C and 72°C respectively.

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Additional file 2:

Target organisms for 40-mer probes and actual tested microarray specificity using optimum hybridisation and washing conditions. Complete list of 40-mer probes used in this study with tested specificity results described for the optimum hybridisation and first washing temperatures of 65°C and 72°C respectively.

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Additional file 3:

Target organisms for 16–21-mer probes and actual tested microarray specificity. Fifty-two short oligonucleotides (16–21-mer) selected for the pilot microarray. Described specificity testing results are for the optimum hybridisation and first washing temperatures of 58°C and 58°C respectively.

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Additional file 4:

Oligonucleotide probes, mainly between 16- and 21-mer in length, used for the expanded community microarray. Unique oligonucleotide probes mainly 16–21-mer in length designed for the short community microarray. Complete list of 230 short oligonucleotide probes used in this study including the predicted specificity.

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Additional file 5:

Microarray binding levels of the entire 16–21-mer microarray probes from healthy individuals and a UC sufferer. Complete set of normalised data values from three healthy individuals (A, B and C) and an Ulcerative Colitis patient in the active disease and remission states. Entire list of binding levels from the short oligonucleotide probes for healthy individuals (designated A, B, C) and the UC sufferer in the disease and remission states.

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