pmartR Software Overview The pmartR package provides a single software tool for QC (filtering and normalization), exploratory data analysis (EDA), and statistical analysis (robust to missing data) and includes numerous visualization capabilities of mass spectrometry (MS) omics data (proteomic...
PerCon SFA Project Publication Linked Data Catalog (uploads pending) The Persistence Control of Engineered Functions in Complex Soil Microbiomes Project (PerCon SFA), at Pacific Northwest National Laboratory (PNNL) is a Genomic Sciences Program, Biosystems Design, Research Science Focus Area project...
"Visualizing the Hidden Half: Plant-Microbe Interactions in the Rhizosphere" Plant roots and the associated rhizosphere constitute a dynamic environment that fosters numerous intra- and interkingdom interactions, including metabolite exchange between plants and soil mediated by root exudates and the...
Multi-Omics Extended Data Package DOI Rapid Remodeling of the Soil Lipidome in Response to a Drying-Rewetting Event This study reveals specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting...
"Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules" The soil microbiome represents one of the most complex microbial communities on the planet, encompassing thousands of taxa and metabolic pathways, rendering holistic analyses computationally intensive and difficult. Here...
Soil samples were collected in triplicate in the fall of 2017 across the three grassland locations having differences in historical annual precipitation field site locations (WA, IA, KS). For each location, one deeply sequenced composite metagenome was obtained to detect viral contigs using a...
Soil samples were collected in triplicate in the fall of 2017 across the three grassland locations having differences in historical annual precipitation field site locations (WA, IA, KS). For each location, one deeply sequenced composite metagenome was obtained to detect viral contigs using a...
KS4A-Omics1.0_FspDS68 Fungal Monoisolate Multi-Omics Data Package DOI "A mineral doped micromodel platform demonstrates fungal bridging of carbon hotspots and hyphal transport of mineral derived nutrients" Molecular mechanisms underlying fungal mineral weathering and nutrient translocation in low...
Influenza A Experiment ICL105 Processed Omics Data Unavailable The purpose of this experiment was to evaluate the host epigenetic response to Influenza A (H5N1) viral infection from human lung adenocarcinoma cells (Calu-3) sample data. Related Experimental Data BioProject: PRJNA428999 GEO Accession...
Influenza A Experiment ICL106 Processed Omics Data Unavailable The purpose of this experiment was to evaluate the human host epigenetic response to Influenza A H5N1 virus and MERS-CoV viral infection from human lung adenocarcinoma cell (Calu-3) high throughput sequencing (MeDIP-Seq) sample data...
Soil fungi facilitate the translocation of inorganic nutrients from soil minerals to other microorganisms and plants. This ability is particularly advantageous in impoverished soils, because fungal mycelial networks can bridge otherwise spatially disconnected and inaccessible nutrient hotspots...
Influenza A Experiment IM104 Processed Omics Data Unavailable This Influenza experiment evaluated mouse lung expression after etoposide treatment and infection with a pandemic H1N1 influenza strain. Related Experimental Data BioProject: PRJNA382278 GEO: GSE97555 (mRNA transcriptome response)...
Ebola Experiment EIHH002 Processed Omics Data Unavailable This experiment evaluated Immortalized Human Hepatocyte (IHH) cell line host response to response to genetically-reconstructed Zaire Ebola virus infection. Transcriptomics Expression profiling by array (mRNA) Non-coding RNA profiling by array...
Ebola Experiment EIHH001 Processed Omics Data Unavailable This experiment evaluated Immortalized Human Hepatocyte (IHH) cell line host response to wild-type Ebola viruses Zaire Ebola (ZEBOV '76) and Reston Ebola (REBOV '08) viral infection. Transcriptomics Expression profiling by array (mRNA) Non...