PerCon SFA Project Data Catalog Collection (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. The PerCon SFA is exploring how environmental niches can be sculpted using the mechanisms of genome reduction and metabolic addiction to drive secure rhizosphere community design for robust biomass cropping in challenging environments.
The PNNL DataHub PerCon SFA project repository contains publication-relevant digital dataset and metadata DOI packages, enabling exploration and download of integrated experimental dataset catalogs publicly available to a global scientific community. and metadata repository allow for exploring and downloading integrated experimental biodesign omics dataset catalogs, including experimental protocols and/or workflows, raw and/or processed data, as required by the repository, and other relevant supporting materials and/or metadata required for research reproducibility and reporting. Capability data have been deposited at community recognized public database(s) where appropriate and are the recorded factual material accepted by the scientific community necessary to validate the resulting publication of information consistent with intellectual property provisions under which the publishable information was produced.
- Genomic Science Program (GSP) Biosystems Design Project Homepage
- PerCon SFA Software Developer Community Collection on Zenodo
- PerCon SFA DOE Systems Biology Knowledgebase (KBase) Collaboration
Data Source Instrument Acquisitions
- Mass Spectrometry (LC-MS)
- Mass Spectrometry (LC/GC-MS)
- Illumina Sequencing (MiSeQ, HiSeQ 4,000)
- PacBio Sequencing (Sequel II)
- X-Ray Computed Tomography (XCT)
Data Standards & Accessibility (unprocessed raw data)
- Genomics: Sequencing data and metadata have been deposited at the JGI Genomes OnLine Database (GOLD) portal, Integrated Microbial Genomes and Microbiomes (IMG/M) portal, and the genomic data sequence archive GenBank.
- Transcriptomics: Sequencing raw read sequence file BioProject and BioSample collections have been deposited at the NCBI Sequence Read Archive (SRA).
- Proteomics, Metabolomics: Mass spectrometry omics acquisition data have been deposited the HUPO Proteomics Standard public community repository Mass Spectrometry Interactive Virtual Environment (MassIVE), for accessible browsing and reuse leveraging the Global Natural Products Social Molecular Networking (GNPS) analysis tool.
- Spectroscopy: X-ray computed tomography images were made available for user access by the EMSL NEXUS data portal corresponding to the processed imaging DOI downloads herein (both input/output data and transformed reconstruction imaging analysis).
- Software/Code: Digital data assets and/or specialized tools required for data reuse are openly available at GitHub and the PNNL PerCon SFA Developer Community collection at Zenodo.
DOE Funding Acknowledgment
The provided material is based upon work supported by the U.S. Department of Energy, Office of Biological and Environmental Research, Genomic Science Program (https://genomicscience.energy.gov) and is a contribution of the Pacific Northwest National Laboratory (PNNL) Secure Biosystems Design Science Focus Area "Persistence Control of Engineered Functions in Complex Soil Microbiomes" project. A portion of this research was supported by the EMSL user project award 10.46936/cpcy.proj.2021.60242/60007227, using instrument capabilities operating under the Environmental Molecular Sciences Laboratory (EMSL), DOE Office of Science User Facility, sponsored by the Biological and Environmental Research program operating under Contract No. DE-AC05-76RL01830.
RDM Curation: Lindsey Anderson (Last updated: 2022-08-19T16:46:57+00:00)