Appendix C. Graphical and tabular views of fungal habitat preferences as revealed by ordinations and environmental correlations.

Graphical and tabular views of fungal habitat preferences as revealed by ordinations and environmental correlations

Appendix A. Site coordinates, sampling information, and F:P ratios across sites.

Site coordinates, sampling information, and F:P ratios across sites

Supplement 1. Three files containing BLAST identifications for fungal OTUs and abundances across samples.

<h2>File List</h2><div> <p><a href="Blast_IDs.csv">Blast_IDs.csv</a> (MD5: 62e5100c20160c284f4d0c0d7e966652)</p> <p><a href="OTU_by_site_matrix.csv">OTU_by_site_matrix.csv</a> (MD5: fd8cb6e0180fda1c17b283fb1bb9de0e)</p> <p><a href="Phyla_Guild_Assignments.csv">Phyla_Guild_Assignments.csv</a> (MD5: 835a54ac9732fb782bc6756fd8e10fa6)</p> </div><h2>Description</h2><div> <p>Blast_IDs is a comma-delimited spreadsheet with a row for each OTU encountered in this study. The columns are as follows: Rank = the relative abundance of that OTU across the entire dataset. Rank #1 was the most abundant OTU (in terms of number of clone sequences falling into that OTU). Operational Taxonomic Unit = the code assigned to that OTU when the sequences were clustered using Cap3. Representative Clone = the code for the original clone sequence that was chosen to represent that OTU. Best Match GenBank Accession = the accession number for the sequence in GenBank with the highest bit score when the OTU representative sequence was blasted against our in-house database. Best Match Description = edited text from the title of the top GenBank blast hit meant to convey the putative identity. Percent Identity = the percent of identical bases over the region of the query and hit that were sufficiently similar to be aligned by BLAST. Length of Overlap = the length of the region that was sufficiently similar to be aligned by BLAST. Bit Score = the quality of the match assigned by BLAST. Quality of Top Match = the taxonomic level to which the query sequence could be identified based on a set of rules involving percent identity combined with overlap length, as described in the text of the article.</p> <p>OTU_by_site_matrix is a comma-delimited spreadsheet providing OUT abundances. Counts of clones belonging to a particular OTU in each sample (site × year × horizon combination) are given. Each row represents one OTU. The site is designated by the first number (e.g., '109'), the horizon by M = mineral and O = organic and the sampling year by 4 = 2004 and 5 = 2005. The first column gives the OTU designation, the second column gives the rank of that OTU and subsequent columns give the clone counts in each sample. The last column provides a cumulative total clone count for each OTU. </p> <p>Phyla_Guild_Assignments is a comma-delimited spreadsheet showing the guilds that were assigned to particular fungal OTUs. The first five columns are identical to those described above for the file Blast_IDs. The next columns, labeled “Phylum or Subphylum” and “Order” give the corresponding GenBank taxonomy designations for the top BLAST match. The last column, labeled “Guild”, provides our best estimate of the trophic guild to which the OTU belongs. ECM = ectomycorrhizal; sap = saprotrophic (typically wood or litter decay); lichen = lichen; ?? = unknown. We only attempted to define guild for a subset of well-defined OTUs.</p> </div

V, D, and J segment use in mouse is also highly uneven.

<p>Lines indicate cumulative distributions (measured on right-hand side y-axis) (a)–(c). Out of space considerations only V segments present at ≥1% are shown. Insets show cumulative distributions. VDJ combinations also appear unevenly, with the ∼200 most frequent VDJ combinations responsible for 50 percent of all recombination events (d).</p

Number of Reads and Clusters.

<p>Number of Reads and Clusters.</p

V, D, and J segment use in human is highly uneven.

<p>Lines indicate cumulative distributions (measured on right-hand side y-axis) (a)–(c). Not all V segments are labeled on the x-axis. V, D, and J segments appear at similar frequencies in two different human subjects (d)–(f). Each point corresponds to a single segment. Insets show cumulative distributions. VDJ combinations also appear unevenly, with the 100 most frequent VDJ combinations responsible for 50 percent of all recombination events (g).</p

Chromosomal alignment of genes.

<p>a) Reads aligning to coding genes were mapped back to the human chromosomes and represented as the % reads aligning to each chromosome. All chromosomes of the human genome are represented within the urinary microvesicles including the mitochondrial chromosome (M). Solid bars – +DNase sample, lined bars – -DNase sample. b) Correlation of reads aligning to coding genes in the +DNase and -DNase samples suggests little if any DNA was present (R² = 0.9664).</p

Analysis of the top 50 genes found in urinary exosomes.

<p>The top 50 most highly expressed genes were determined and grouped in terms of function or name. a) In the +DNase sample 76% of genes were related to ribosomal proteins and a further 6% related to translation regulation. Other genes related to ferritin, prostate specific genes, cell regulation and novel genes were also featured. A similar distribution was also seen for the -DNase sample (b). In both instances the TPT1 gene was the most abundantly expressed gene.</p

Top 10 expressed ncRNA in microvesicles (+DNase).

<p>The most abundantly expressed ncRNA as defined by the RNAdb <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096094#pone.0096094-Pang1" target="_blank">[14]</a> are listed by number of reads present in the microvesicle population, the RNAdb ID, ncRNA name and accession ID number as identified in the DNase treated sample.</p

Mapping of coding genes to the genitourinary epithelium.

<p>a) Cartoon of the genitourinary system, highlighting specialized regions including the glomerulus (1), proximal tubules (2), medullary thick ascending limb (3), distal convoluted tubule (4), collecting duct (5), bladder (6) and prostate (7). b) The number of deep sequencing reads normalized to gene length were graphed to produce a transcriptional profile for each of the sub-regions of the genitourinary tract (solid bars – +DNase, lined bars – -DNase).</p