Escherichia coli (ID 230919) - BioProject

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Accession: PRJNA230919 ID: 230919

Escherichia coli

GenomeTrakr umbrella project for Escherichia coli and Shigella sp.

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This project is a component of the GenomeTrakr umbrella project

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22 additional projects are components of the GenomeTrakr umbrella project.

This umbrella project holds a set of data bioprojects, each representing a laboratory sequencing E. coli (with a focus on STECs) and Shigella sp. in collaboration with GenomeTrakr's open genomic epidemiology surveillance effort for the real-time monitoring of foodborne pathogens. Automated clustering and genotyping results for these data can be found at NCBI Pathogen Detection (link below).

Accession	PRJNA230919
Type	Umbrella project
Keyword	GMI
Publications	Timme RE et al., "Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens.", One Health Outlook, 2020;2(1):20
Submission	Registration date: 9-Dec-2013 FDA/CFSAN
NCBI Links	NCBI Pathogen Detection
Related Resources	FDA whole genome sequencing program NCBI Pathogen FTP for current phylogenetic trees E. coli Outbreaks Whole Genome Sequencing (WGS) Fast Facts FDA GenomeTrakr Video
Relevance	Medical

Project Data:

Resource Name	Number of Links
Sequence data
Nucleotide (total)	676308
WGS master	28487
Genomic DNA	85
SRA Experiments	29647
Protein Sequences	2482066
Publications
PubMed	12
PMC	11
Other datasets
BioSample	31633
Assembly	28516

SRA Data Details

Parameter	Value
Data volume, Gbases	14,634
Data volume, Tbytes	7.54

Escherichia coli encompasses the following 53 sub-projects:

Project Type

Number of Projects

Genome sequencing

Highest level of assembly :

Complete genome
Scaffolds
Contigs
No data links
Total

5
1
37
10
53

BioProject accession	Assembly level	Name	Title
PRJNA230969	Complete genome	Escherichia	GenomeTrakr Project: US Food and Drug Administration (FDA/CFSAN)
PRJNA338676	Contigs	Escherichia	GenomeTrakr Project: Ohio Department of Agriculture \| Animal Disease Diagnostic Laboratory (FDA)
PRJNA675643	Contigs	Escherichia	GenomeTrakr Project: VT Dept. of Health, Escherichia (Vermont Department of Health...)
PRJNA1024537	Contigs	Escherichia	GenomeTrakr Project: University of California, Davis \| School of Veterinary Medicine (FDA Center for Food Safety...)
PRJNA230968	Contigs	Escherichia coli	GenomeTrakr Project: Arizona State Public Health Laboratory (FDA/CFSAN)

List all 53 'Genome sequencing' projects...

BioProject accession	Assembly level	Name	Title
PRJNA230969	Complete genome	Escherichia	GenomeTrakr Project: US Food and Drug Administration (FDA/CFSAN)
PRJNA338676	Contigs	Escherichia	GenomeTrakr Project: Ohio Department of Agriculture \| Animal Disease Diagnostic Laboratory (FDA)
PRJNA675643	Contigs	Escherichia	GenomeTrakr Project: VT Dept. of Health, Escherichia (Vermont Department of Health...)
PRJNA1024537	Contigs	Escherichia	GenomeTrakr Project: University of California, Davis \| School of Veterinary Medicine (FDA Center for Food Safety...)
PRJNA230968	Contigs	Escherichia coli	GenomeTrakr Project: Arizona State Public Health Laboratory (FDA/CFSAN)
PRJNA232925	Contigs	Escherichia coli	GenomeTrakr Project: New York State Dept. of Health, Wadsworth Center (Wadsworth Center / NYSDOH)
PRJNA251752	Contigs	Escherichia coli	GenomeTrakr Project: Virginia - Division of Consolidated Lab. Services (FDA/CFSAN)
PRJNA268206	Contigs	Escherichia coli	GenomeTrakr Project: USDA - Food Safety and Inspection Service (FDA Center for Food Safety...)
PRJNA271299	No data links	Escherichia coli	GenomeTrakr Project: Argentina (FDA Center for Food Safety...)
PRJNA277984	Contigs	Escherichia coli	GenomeTrakr Project: California Department of Health - FDLB Micro (US Food and Drug Administration)
PRJNA282762	Contigs	Escherichia coli	GenomeTrakr: Argentina (US Food and Drug Administration)
PRJNA284275	Contigs	Escherichia coli	GenomeTrakr Project: Texas Department of State Health Services (FDA)
PRJNA283914	Contigs	Escherichia coli	GenomeTrakr Project: Washington State Department of Health (Washington State Department...)
PRJNA292570	Contigs	Escherichia coli	GenomeTrakr Project: New Mexico State University, Food Safety Laboratory (US Food and Drug Administration)
PRJNA293225	Scaffolds	Escherichia coli	GenomeTrakr Project: Thakur Molecular Epidemiology Laboratory, NC State University (US Food and Drug Administration)
PRJNA298331	Contigs	Escherichia coli	GenomeTrakr Project: Florida Department of Health, University of Florida (US Food and Drug Administration)
PRJNA299490	Contigs	Escherichia coli	GenomeTrakr Project: SDSU Veterinary & Biomedical Sciences/ DOH South Dakota (US Food and Drug Administration)
PRJNA302269	No data links	Escherichia coli	GenomeTrakr project: FDA-CFSAN, Moffett Center (US Food and Drug Administration)
PRJNA306263	Contigs	Escherichia coli	GenomeTrakr project: Alaska State Public Health Laboratory-Anchorage (FDA)
PRJNA311907	Contigs	Escherichia coli	GenomeTrakr Project: Minnesota Department of Health (FDA)
PRJNA312475	Complete genome	Escherichia coli	GenomeTrakr Project: FDA-CFSAN MDP Escherichia coli survey from foods (FDA)
PRJNA329615	Contigs	Escherichia coli	GenomeTrakr Project: Florida Department of Agriculture (FDA)
PRJNA338681	Contigs	Escherichia coli	GenomeTrakr Project: State Hygienic Laboratory at the University of Iowa (FDA)
PRJNA342435	Contigs	Escherichia coli	GenomeTrakr Project: Joint Institute for Food Safety and Applied Nutrition (FDA)
PRJNA342957	No data links	Escherichia coli	GenomeTrakr Project: NSU- Halmos College of Natural Sciences and Oceanography_Microbiology & Genetics Laboratory (FDA)
PRJNA357722	Contigs	Escherichia coli	GenomeTrakr Project: Penn State University \| Department of Food Science \| Dudley Lab (FDA)
PRJNA357822	Contigs	Escherichia coli	GenomeTrakr Project: NSF International \| Applied Research Center (FDA)
PRJNA358244	Contigs	Escherichia coli	GenomeTrakr project: FDA-CFSAN, IFSH (FDA)
PRJNA368991	Contigs	Escherichia coli	GenomeTrakr Project: Michigan Department of Agriculture and Rural Development \| Geagley Laboratory (FDA)
PRJNA369528	No data links	Escherichia coli	GenomeTrakr Project: Massachusetts Department of Public Health (FDA)
PRJNA319594	Contigs	Escherichia coli	GenomeTrakr project: Escherichia coli/Shigella, MDU PHL, Australia (Microbiological Diagnostics...)
PRJNA541972	Complete genome	Escherichia coli	GenomeTrakr Project: U.S. Food and Drug Administration - CFSAN (FDA Center for Food Safety...)
PRJNA578396	No data links	Escherichia coli	GenomeTrakr Project: Kentucky Department for Public Health (FDA Center for Food Safety...)
PRJNA591008	Complete genome	Escherichia coli	GenomeTrakr Project: Maryland Department of Health and Mental Hygiene (FDA Center for Food Safety...)
PRJNA613831	Contigs	Escherichia coli	GenomeTrakr Project: Washington State Department of Agriculture (Washington State Department...)
PRJNA631029	Contigs	Escherichia coli	Bornstein-Forst Laboratory - Marian University - Escherichia coli from Bovine reservoirs (FDA Center for Food Safety...)
PRJNA665053	No data links	Escherichia coli	Escherichia coli Genome sequencing (NCSU-CVM)
PRJNA670174	Contigs	Escherichia coli	South Carolina Department of Health Escherichia coli Genome sequencing and assembly (South Carolina Dept. of Health...)
PRJNA675629	Contigs	Escherichia coli	GenomeTrakr Project: Michigan Department of Health and Human Services (Michigan Department of Health...)
PRJNA677988	Contigs	Escherichia coli	GenomeTrakr Project: U.S. Food and Drug Administration - CFSAN (FDA Center for Food Safety...)
PRJNA731476	No data links	Escherichia coli	Genome Trackr Project: IN Department of Health (IN Department of Health Submission...)
PRJNA745210	Contigs	Escherichia coli	Escherichia coli SENASICA MX (SENASICA)
PRJNA774259	Contigs	Escherichia coli	GenomeTrakr Project: NJ Department of Agriculture, Animal Health Diagnostic Laboratory (New Jersey Department of...)
PRJNA800432	Contigs	Escherichia coli	GenomeTrakr Project: Escherichia coli, Missouri State Public Health Laboratory (Missouri State Public Health...)
PRJNA826489	Contigs	Escherichia coli	GenomeTrakr Project: West Virginia Department of Agriculture (Megan Young)
PRJNA832234	Contigs	Escherichia coli	GenomeTrakr Project: Kansas State University (GenomeTrakr Project: Massachusetts...)
PRJNA979937	Contigs	Escherichia coli	GenomeTrakr Project: State of New Hampshire Public Health laboratories (PulseNet Next Generation...)
PRJNA1045654	Contigs	Escherichia coli	Genomic Characterization of Environmental Escherichia coli from the Shenandoah Valley of Virginia (Virginia Division of Consolidated...)
PRJNA758973	No data links	Escherichia coli and Shigella	Genome Trakr Project: Rhode Island Department of Health (Rhode Island State Health...)
PRJNA415804	Contigs	Escherichia coli/Shigella species	GenomeTrakr Project: New York State Department of Agriculture and Markets (NYAG) (FDA)
PRJNA947175	No data links	Escherichia sp.	GenomeTrakr Project: Escherichia sp., Minnesota Department of Health (Minnesota Department of Health...)
PRJNA273284	Complete genome	Shigella	GenomeTrakr Project: US Food and Drug Administration - CFSAN (FDA Center for Food Safety...)
PRJNA670176	No data links	Shigella	South Carolina Department of Health Shigella Genome sequencing and assembly (South Carolina Dept. of Health...)

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GenomeTrakr umbrella project for Escherichia coli and Shigella sp.

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