Additional file 1: of Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi

contains supplemental table 1, which summarize count of the reads of plant miRNAs found within each sample. (CSV 2 mb

Additional file 1: of Biclustering of transcriptome sequencing data reveals human tissue-specific circular RNAs

One hundred forty-eight thousand ninety-five unique back-splicing junctions were identified from the selected transcriptome sequencing runs. Each of the junction site satisfy the threshold defined in the find_circ scripts. (XLSX 10182 kb

Additional file 2: of Biclustering of transcriptome sequencing data reveals human tissue-specific circular RNAs

The biclustering algorithm clustered 16,317 unique junctions into 66 coherent expression profile models. (RAR 1442 kb

Groups of enriched gene ontology (GO) terms for differentially expressed genes common to both trisomy 2 and tertiary trisomy 2.

<p>The gene ontology was analyzed by use of AgriGO <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114617#pone.0114617-Du1" target="_blank">[33]</a>.</p>a<p>Biological process (P); molecular function (F).</p>b<p>Chi-square statistical test; FDR, false discovery rate.</p><p>Groups of enriched gene ontology (GO) terms for differentially expressed genes common to both trisomy 2 and tertiary trisomy 2.</p

The <i>aur2-1</i>/+ is tertiary trisomy 2 revealed by array comparative genome hybridization (array CGH).

<p>(<b>A</b>) The log₂ ratios of signal intensity of <i>Arabidopsis</i> chromosomes in trisomics (<i>AAA</i> or <i>AAa</i>) to wild-type diploids (Col-0). Each dot indicates one set of probes corresponding to a unique position on the chromosomes (Chr.). Locations of centromeres are the area with fewer dots. Shaded area in chromosome 2 indicates the region containing the translocation breakpoint. (<b>B</b>) A schematic representation of chromosome 2 in <i>aur2-1</i>/+. S, short; L, long arm of chromosomes. (<b>C</b>) The log₂ ratios of signal intensity of chloroplast and mitochondria genomes in trisomy (<i>AAA</i> or <i>Aaa</i>) to wild-type diploid (Col-0). Genome duplication is identified by the ratio shifting above the baseline at 0. The moving average is a series of averages of 10 probe sets.</p

Whole-genome transcriptome analysis in trisomic plants.

<p>(<b>A</b>) The log₂ ratios of the expression of all genes in trisomics (<i>AAA</i> or <i>AAa</i>) relative to wild-type diploids (Col-0). Each dot indicates one set of probes corresponding to a unique position on the chromosomes (Chr.). Positive and negative values indicate upregulated and downregulated expression, respectively. Locations of centromeres are the area with no gene expression. (<b>B</b>) Venn diagram shows the specific and overlapping genes with significant misregulated expression compared to wild-type diploid (Col-0) between trisomy 2 (<i>AAa</i>) and tertiary trisomy 2 (<i>AAA</i>) (<i>p</i><0.05). (<b>C</b>) Clustering and heat map of the 325 misregulated genes common to the two trisomics (<i>AAA</i> and <i>AAa</i>). Four groups of genes based on expression patterns are shown on the right.</p

The <i>aur2-1</i>/+ mutant is trisomy 2.

<p>(<b>A</b>) Rosette phenotype of wild type (Col-0) and progeny from self-fertilized <i>aur2-1</i>/+. W, wild-type rosette leaves; R, round-shaped rosette leaves; T, tiny rosette leaves. (<b>B</b>) Metaphase spreads of the mitotic cells from Col-0 and <i>aur2-1</i>/+. (<b>C</b>) Meiosis in pollen mother cells of Col-0 and <i>aur2-1</i>/+. DAPI-stained chromosomes in different meiotic stages. Yellow arrows, extra univalents; red arrow, pentavalent; yellow stars, extra sister chromatids. (<b>D</b>) Fluorescence <i>in situ</i> hybridization analysis of <i>aur2-1</i>/+. Metaphase spreads of the <i>aur2-1</i>/+ mitotic cells probed with FITC-labeled 45S rDNA (green) and rhodamine-labeled 5S rDNA (red). Dashed lines, outline of DAPI-stained chromosome. Scale bar in (<b>A</b>) 2 cm; (<b>B</b>) 5 µm; (<b>C</b>) 10 µm; (<b>D</b>) 2 µm.</p

Gene ontology (GO) terms enriched among the misregulated genes in three trisomic plants.

<p>The specific enriched GO terms for up- and downregulated genes in <i>AAA</i> (white), <i>AAa</i> (black) and trisomy 5 (gray) were derived by use of agriGO <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114617#pone.0114617-Du1" target="_blank">[33]</a>. The <i>p</i> values for GO terms are shown in –logarithmic scale. Data for trisomy 5 are from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114617#pone.0114617-Huettel1" target="_blank">[5]</a>. Complete lists are presented in Tables S3 and S4 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114617#pone.0114617.s001" target="_blank">S1 File</a>.</p

Genetic analysis of <i>aur2-1</i>/+ inheritance.

a<p>HZ, heterozygous.</p>b<p>HM, homozygous.</p><p>Genetic analysis of <i>aur2-1</i>/+ inheritance.</p

A Model of the genomic constitution of <i>aur2-1</i>/+ <i>qrt2-1</i>/<i>qrt2-1</i> tetrads.

<p>Meiosis without (<b>A</b>) or with crossing over (<b>B</b>). Left panel shows pollen mother cells and right panel, tetrads after meiosis. Chromosome 2 carrying the wild-type <i>AUR2</i> (<i>A</i>) is shown in a blue line or the <i>aur2-1</i> allele (<i>a</i>) with a translocation is indicated in a bold red line. M I, meiosis I; M II, meiosis II; shaded cells, aborted pollen grains.</p