Array. Each column represent a different sample, whose identification is reported as its label. On the left, the ZipCode, the probe name and ID are reported. “”Type”" is a numeric flag used for the classification of the probes: 1 is the hybridization control, 2 is the ligation control, 3 Go6983 chemical structure indicates the HTF-Microbi.Array probes, 4 are the unused ZipCodes and 5 is the Blank. “”Numeric ID”"
is given to the probes according to their “”type”" and “”Oligo ID”" values. (XLS 104 KB) Additional file 4: Sensitivity tests of the HTF-Microbi.Array. Raw data of the sensitivity tests on the HTF-Microbi.Array. The workbook has two spreadsheets: “”Artificial mix data”", reporting the results of the serial ABT-737 solubility dmso dilutions of the 6 bacterial DNA mix (B. cereus, L. casei, B. adolescentis, R. albus, Prevotella, Y. enterocolitica), with concentrations ranging from 50 to 0.7 fmol. “”Absolute sensitivity E. coli”" spreadsheet reports the results of the tests on low quantities of E. coli 16S amplicon in increasing amounts of human genomic DNA. The file is structured as described above for Additional file 3. (XLS 68 KB) Additional file 5: Tests of the HTF-Microbi.Array on faecal samples. Raw data for the experimental characterization of the faecal microbiota of eight healthy young adults. Patient ID and replicate number are reported as the column headers.
The file is structured as described above for Additional file 3. (XLS 52 KB) Additional file 6: Universal array scheme. Graphical representation
of the Universal Array platform. Each array has 8 identical subarrays (A), which can be addressed click here independently. Each subarray is made by 208 spots, with quadruplicates of each ZipCode (B); hybridization and ligation controls and Blanks are repeated 8, 6 and 6 times, respectively; the figure highlights in gray the ZipCodes actually associated to probe pairs used in the HTF-Microbi.Array. Sequences (5′ – 3′ oriented) and numbers of the ZipCodes are reported in (C). (PDF 19 KB) References 1. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE: Metagenomic analysis of the human distal gut microbiome. Science 2006,312(5778):1355–9.PubMedCrossRef 2. Ley RE, Arachidonate 15-lipoxygenase Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI: Evolution of mammals and their gut microbes. Science 2008,320(5883):1647–51.PubMedCrossRef 3. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI: The human microbiome project. Nature 2007,449(7164):804–10.PubMedCrossRef 4. Egert M, de Graaf AA, Smidt H, de Vos WM, Venema K: Beyond diversity: functional microbiomics of the human colon. Trends Microbiol 2006,14(2):86–91.PubMedCrossRef 5. Neish AS: Microbes in gastrointestinal health and disease. Gastroenterology 2009,136(1):65–80.PubMedCrossRef 6.