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Sample processing was performed as previously reported (Parashar et al. 2004).
Further sample processing was performed according to Thies-Flechtner et al. [10].
To enumerate E. coli numbers, sample processing was performed within 24 hours of sample collection.
Sample processing was performed as described previously [24].
All sample processing was performed under BSL-3 conditions.
Sample processing was performed with an Affymetrix GeneChip Fluidics Station FS450 and arrays were scanned with a GCS300 array scanner according to manufacturer's recommendations.
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Sample collection and processing was performed as previously described [42].
All testing and sample collection or processing was performed by individuals unaware of the treatment group of the animals.
All sample labeling and GeneChip processing was performed at the London Regional Genomics Centre Robarts Research Institutee, London, Ontario, Canada; http://www.lrgc.ca).
All methylated DNA immunoprecipitation (MeDIP), sample labeling, hybridization and processing was performed at the Arraystar Inc. (Rockville, MD).
Muscular tissue samples preparation and microarray processing was performed according to Affymetrix Gene Expression Analysis Technical Manual.
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