ECAY transcripts in stallion sperm.

<p>Agarose gel images showing RT-PCR amplicons of 7 ECAY genes and transcripts in stallion sperm.</p

Distribution and expression of mapped RNA sequence tags in the horse genome.

<p><b>Mb</b>–megabase-pair; <b>AC</b>–average coverage; <b>Mt</b>–mitochondrial genome; map information for horse chromosomes was retrieved from Ensemb (<a href="http://www.ensembl.org/index" target="_blank">http://www.ensembl.org/index</a>. html); * includes known and novel protein coding, miRNA, rRNA, snRNA, snoRNA and Misc RNA genes.</p

Comparison of RNA-seq data with current equine gene models:

<p>(a) <i>PKM2</i> showing 9 <i>in silico</i> prediction sites, of which two are positioned 5′ upstream to exon 1; (b) <i>CRISP3</i> with 3 <i>in silico</i> prediction sites, all located 5′ upstream to exon 1; (c) <i>PRM1</i> and <i>TNP2</i> cluster (the protamine cluster) with 12 <i>in silico</i> prediction sites of which only two align with <i>PRM1</i> and <i>TNP2</i> exons. Black boxes with numbers –exons in current gene models; blue boxes –very highly expressed tags (AC≥100); red boxes–highly expressed tags (10</p

Summary statistics for mapped RNA sequence tags

<p>: (<b>a</b>) Comparison of mapped tags (AC≥1) between the two sperm samples; (<b>b</b>) Proportions of tags with very high (AC≥100), high (10</p

Venn diagram of transcripts detected in stallion sperm and testes by microarray analysis (SNR ≥2).

<p>Venn diagram of transcripts detected in stallion sperm and testes by microarray analysis (SNR ≥2).</p

Structural and functional annotations for mRNAs and ESTs with the highest AC values by RNA-seq.

<p>Structural and functional annotations for mRNAs and ESTs with the highest AC values by RNA-seq.</p

Results of quantitative PCR assays for selected bacterial groups.

<p>H = healthy, NHD = acute non-hemorrhagic diarrhea, AHD = acute hemorrhagic diarrhea, A_IBD = active IBD, S_IBD = therapeutically controlled, clinically insignificant IBD. Columns not sharing a common superscript are significantly different (P<0.05).</p

Oligonucleotides primers/probes used in this study.

<p>Oligonucleotides primers/probes used in this study.</p

<i>Faecalibacterium</i> spp. and the phylum Fusobacteria in active and non-active IBD.

<p>Using qPCR, paired fecal samples were analyzed from dogs (n = 8) at time periods of active and clinically insignificant IBD as scored by a clinical IBD disease activity index (CIBDAI). The time period between the collections of repeated samples ranged from 2–8 months (median 5.5 months). None of the other bacterial groups evaluated by qPCR, including total bacteria, revealed significant differences between the paired time periods.</p

Principal Coordinates Analysis (PCoA) of unweighted UniFrac distances of 16 S rRNA genes.

<p>(A) Analysis for healthy dogs (blue), dogs with acute non-hemorrhagic diarrhea (NHD; green), and dogs with acute hemorrhagic diarrhea (AHD; red). These results indicate that fecal microbial communities differ in dogs with acute forms of diarrhea compared to healthy control dogs. Statistical analysis revealed a significant separation between samples obtained from NHD and AHD (ANOSIM; p = 0.004) and both groups were also significantly different from the healthy dogs (ANOSIM; NHD vs. healthy dogs, p = 0.003; AHD vs. healthy dogs, p = 0.001). (B) Analysis for healthy dogs (blue), dogs with active IBD (red), and dogs with therapeutically controlled IBD (green). In contrast to the dogs with acute diarrhea, fecal communities in dogs with chronic forms of diarrhea (active idiopathic IBD) were not significantly different from healthy dogs in this study.</p