37 research outputs found

    Additional file 3: of Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

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    Rarefaction based on known taxa. The figure shows the numbers of taxa calculated from samples of sequence data used for constructing the HITdb. Boxplots showing the numbers of found species (A) and genera (B) at two sample sizes (about 90¬†% and 80¬†% of sequences, n‚ÄČ=‚ÄČ9 and n‚ÄČ=‚ÄČ10, respectively). The horizontal red dashed line shows the number of OTUs in all sequences (100¬†% of sequences). (PDF 52¬†kb

    Additional file 1: of Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

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    Phylogenetic trees. Package containing Newick and figure files of bacterial and archaeal phylogenies in HITdb. (PDF 22521√ā¬†kb

    Additional file 4 of Blood donor biobank and HLA imputation as a resource for HLA homozygous cells for therapeutic and research use

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    Additional file 4: Table 4. Additional Table 4 HLA allele count and allele frequencies in imputed data set (N = 20737). Corresponding known HLA allele frequencies in Finland (Stem Cell Registry, unpublished data) are shown as reference allele frequencies. No reference allele frequency was available for the alleles HLA-C*17:03 and HLADPB1* 105:01 or for the alleles of which imputation result remained in low resolution level

    Additional file 1 of Blood donor biobank and HLA imputation as a resource for HLA homozygous cells for therapeutic and research use

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    Additional file 1: Figure 1Posterior probabilities of the imputed HLA alleles in a given HLA haplotype. Number of individuals homozygous for each haplotype (1-41) is stated in Table 1. Median, highest and lowest values of posterior probabilities are shown in haplotypes 1-21, and the actual posterior probability value in haplotypes (22-41) where one individual was identified

    Additional file 2 of Blood donor biobank and HLA imputation as a resource for HLA homozygous cells for therapeutic and research use

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    Additional file 2: Table 2. Comparison of clinical grade and imputed HLA typing result. Altogether clinical grade result was available in 27,588 typings of 13,794 individuals of the present study. Only typing results where discrepancies occurred are shown in this table

    Additional file 1: Table S1. of Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phase

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    Numbers of CDS- mapped reads per samples, used for the analysis. Table S2. The list of predicted putative adhesins in L. oligofermentans genome. Table S3. Predicted carbohydrate/carbon source catabolic/transport genes in L. oligofermentans genome. Table S4. Criteria for classifying genes into groups with different expression patterns. Table S5. The number of differentially expressed genes containing CcpA- binding site in the upstream regions for pairwise and triplewise comparisons between growth conditions. Table S6. Motif sequence LOGOs, discovered and enriched in the upstream regions of the co-regulated genes. Figure S1. Genome map of L. oligofermentans LMG 22743T. Figure S2. Venn diagrams representing the numbers of differentially expressed genes for pairwise and triplewise comparisons between growth conditions at 20 h (A), 24 h (B) and 30 h (C). Figure S3. RPKM plots for the putative glucose (manXYZ), xylose (XylT) and ribose (deoP and rbsACB) transporters. Figure S4. Aerobic growth on glucose, ribose and xylose, supplemented with heme or menaquinone or both. (PDF 953 kb

    The principle of ligation detection reaction.

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    <p>The discriminating probe (DP) and the common probe (CP) are designed to hybridize adjacently on the template DNA and are joined by ligase in the presence of a matching template (HPV PCR product). The discriminating 3′ base can be A, C, T or G. The reaction is thermally cycled and ligation products addressed on microarray spots by the unique ZipCode sequences flanking each CP. Hybridization control probe carries a different label (6-Fam) than the DP (Cy3).</p

    Specificity of HPV LDR probe pool.

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    <p>The HPV LDR probe pool was tested against individual plasmid templates. The horizontal axis shows the probes by ZipCodes and corresponding HPV types. The vertical axis shows plasmid templates by HPV type. The signals are medians over spot replicates on 1‚Äď3 microarrays. The majority of the probes give a high hybridization signal only for their specific target plasmids. For HPV 11, 42 and 43, there are no functional probes. HPVs 39, 56 and 68 have only one functional probe each. The probe A85 (HPV 73 ) shows a strong nonspecific hybridization signal to HPV 44 template. Minor nonspecific hybridisation signals are evident in probes A59, A110, A57 and A56.</p
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