This dataset from maize-GAMER is a new high-coverage and reproducible functional annotation of maize protein coding genes based on Gene Ontology (GO) term assignments that covers all genes in the B73 RefGen_V4 Zm00001d.2.
Vaccination Against Lawsonia intracellularis Decreases Shedding of Salmonella enterica serovar Typhimurium in Co-Infected Pigs and Alters the Gut Microbiome
Salmonella enterica is a leading cause of foodborne illness worldwide and pork can serve a source of infection. In this study, we investigated if vaccinating pigs against Lawsonia intracellularis, a common pathogen of swine that has previously been shown to favor Salmonella enterica infection, confers protection against Salmonella enterica serovar Typhimurium. We investigated the underlying changes in the gut microbiome mediated by single S. Typhiumurium infection compared to co-infection with L. intracellularis as well as the effect of vaccination on the microbiome.
This dataset from maize-GAMER is a new high-coverage and reproducible functional annotation of maize (Zea mays) protein coding genes based on Gene Ontology (GO) term assignments that covers all genes in the B73 RefGen_v3 5b+ set. Data are compressed gzip (.gz) files.
Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans
The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs, to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses.
SNP Genotyping Data from the Barley Experimental Population from "Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley"
The 318 sampled wild barley accensions, known as the Wild Barley Diversity Collection (WBDC), were genotyped using the Illumina Golden Gate Genotyping Assay with two Barley Oligo Pool assay chips (BOPA1 and BOPA2). The genotype calls were based on machine-scored data using the program ALCHEMY and the SNPs were annotated using the program SNPMeta. The BOPA1 & 2 files contains the output of the ALCHEMY program.
These are SNPs on two Illumina GoldenGate genotyping arrays and one 9k iSelect genotyping array.
Changes in the Porcine Intestinal Microbiome in Response to Infection with Salmonella Enterica and Lawsonia Intracellularis
Salmonella enterica is a leading cause of food borne illness. Recent studies have shown that S. enterica is a pathogen capable of causing alterations to the composition of the intestinal microbiome. A recent prospective cross-sectional study of French pork production farms found a statistically significant association between Lawsonia intracellularis and carriage of S. enterica. The ZIP file includes 51 sequence files (FASTA format) and 1 Excel file describing the species, age, sampled tissue, treatment condition, and sample name corresponding to the different file names. The Excel file is converted to a csv for archival purposes. The Readme.txt file describes the context of how the data was created and any codes used in the spreadsheet.
Effort Versus Reward: Preparing samples for fungal community characterization in high-throughput sequencing surveys of soils
This data set consists of four data files. The FASTA file, Representative OTU sequences.fa, contains representative sequences from the operational taxonomic units (OTUs) shown in the OTU table. FASTA files can be opened in simple text editors, and sequences can be aligned using the BLAST tool (http://blast.ncbi.nlm.nih.gov/Blast.cgi) or open source software, like AliView (http://www.ormbunkar.se/aliview/). There are two Excel data files: OTU table and heatmaps.xlsx and Diversity Indexes.xlsx. The former contains the raw abundance data for the observed OTUs from the different experimental sites. The latter is a breakdown of various diversity indices that are grouped based on experimental characteristics, such as extraction volume, extraction method, etc. Excel_Archive.zip is a compressed version of the two Excel data files that have been converted to more archival-friendly formats using Excel Archival Tool.
This dataset presents the Anoplophora glabripennis gene set BCM_v_0.5.3. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Anoplophora glabripennis genome assembly 1.0.