Campylobacter (ID 258021) - BioProject

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Accession: PRJNA258021 ID: 258021

Campylobacter

GenomeTrakr umbrella project for Campylobacter jejuni and Campylobacter coli

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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 these two Campylobacter species 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	PRJNA258021
Type	Umbrella project
Keyword	GMI
Organism	Campylobacter sp.[Taxonomy ID: 205] Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales; Campylobacteraceae; Campylobacter; Campylobacter sp.
Publications	Published online: Timme R 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)
Submission	Registration date: 11-Aug-2014 FDA/CFSAN
NCBI Links	NCBI Pathogen Detection
Related Resources	FDA Whole Genome Sequencing Program (WGS) NCBI Pathogen FTP Whole Genome Sequencing (WGS) Fast Facts FDA GenomeTrakr Video
Relevance	Medical

Project Data:

Resource Name	Number of Links
Sequence data
Nucleotide (total)	11018
WGS master	3368
Genomic DNA	36
SRA Experiments	4599
Protein Sequences	364671
Other datasets
BioSample	4586
Assembly	3400

SRA Data Details

Parameter	Value
Data volume, Gbases	1,229
Data volume, Tbytes	0.64

Campylobacter encompasses the following 32 sub-projects:

Project Type

Number of Projects

Genome sequencing

Highest level of assembly :

Complete genome
Scaffolds
Contigs
SRA or Trace
No data links
Total

3
1
21
2
5
32

BioProject accession	Assembly level	Name	Title
PRJNA1015272	Contigs	CAGED: Campylobacter Genomics and Environmental Enteric Dysfunction	CAGED: Campylobacter Genomics and Environmental Enteric Dysfunction (FDA Center for Food Safety...)
PRJNA258022	Complete genome	Campylobacter	GenomeTrakr Project: FDA-CFSAN (FDA/CFSAN)
PRJNA271861	Contigs	Campylobacter	Campylobacter Genome sequencing and assembly (Fera)
PRJNA293228	Contigs	Campylobacter	GenomeTrakr Project: Thakur Molecular Epidemiology Laboratory, NC State University (US Food and Drug Administration)
PRJNA314999	Contigs	Campylobacter	GenomeTrakr Project: Maryland Department of Health and Mental Hygiene (FDA)

List all 32 'Genome sequencing' projects...

BioProject accession	Assembly level	Name	Title
PRJNA1015272	Contigs	CAGED: Campylobacter Genomics and Environmental Enteric Dysfunction	CAGED: Campylobacter Genomics and Environmental Enteric Dysfunction (FDA Center for Food Safety...)
PRJNA258022	Complete genome	Campylobacter	GenomeTrakr Project: FDA-CFSAN (FDA/CFSAN)
PRJNA271861	Contigs	Campylobacter	Campylobacter Genome sequencing and assembly (Fera)
PRJNA293228	Contigs	Campylobacter	GenomeTrakr Project: Thakur Molecular Epidemiology Laboratory, NC State University (US Food and Drug Administration)
PRJNA314999	Contigs	Campylobacter	GenomeTrakr Project: Maryland Department of Health and Mental Hygiene (FDA)
PRJNA355268	Contigs	Campylobacter	GenomeTrakr Project: Ohio Department of Agriculture Animal Disease Diagnostic Laboratory (FDA)
PRJNA613830	Contigs	Campylobacter	GenomeTrakr Project: Washington State Department of Agriculture (Washington State Department...)
PRJNA670181	Contigs	Campylobacter	South Carolina Department of Health Campylobacter species Genome sequencing and assembly (South Carolina Dept. of Health...)
PRJNA731489	No data links	Campylobacter	Genome Trakr Project: IN Department of Health (IN Department of Health Submission...)
PRJNA774263	No data links	Campylobacter	GenomeTrakr Project: NJ Department of Agriculture, Animal Health Diagnostic Laboratory (New Jersey Department of...)
PRJNA826493	No data links	Campylobacter	GenomeTrakr Project: West Virginia Department of Agriculture (Megan Young)
PRJNA861696	Contigs	Campylobacter	GenomeTrakr Project: State of New Hampshire Public Health laboratories (State of NH Public Health...)
PRJNA274704	Contigs	Campylobacter jejuni	GenomeTrakr Project: State of Alaska Public Health Laboratory (US Food and Drug Administration)
PRJNA296704	Scaffolds	Campylobacter jejuni	GenomeTrakr Project: Texas Department of State Health Services (US Food and Drug Administration)
PRJNA309864	Complete genome	Campylobacter jejuni	GenomeTrakr Project: California Department of Health - FDLB Micro (US Food and Drug Administration)
PRJNA323586	Contigs	Campylobacter jejuni	GenomeTrakr Project: Virginia - Division of Consolidated Laboratory Services (FDA)
PRJNA325644	Contigs	Campylobacter jejuni	GenomeTrakr Project: Washington State Department of Health (FDA)
PRJNA327813	Contigs	Campylobacter jejuni	GenomeTrakr Project: New Mexico State University Food Safety Laboratory (FDA)
PRJNA339715	Contigs	Campylobacter jejuni	GenomeTrakr Project: State Hygienic Laboratory at the University of Iowa (FDA)
PRJNA357725	SRA or Trace	Campylobacter jejuni	GenomeTrakr Project: Penn State University \| Department of Food Science \| Dudley Lab (FDA)
PRJNA368990	Contigs	Campylobacter jejuni	GenomeTrakr Project: Michigan Department of Agriculture and Rural Development Geagley Laboratory (FDA)
PRJNA369525	No data links	Campylobacter jejuni	GenomeTrakr Project: Massachusetts Department of Public Health (FDA)
PRJNA325142	Contigs	Campylobacter sp.	GenomeTrakr Project: New York State Department of Health, Wadsworth Center (None)
PRJNA541966	Complete genome	Campylobacter sp.	GenomeTrakr Project: U.S. Food and Drug Administration - CFSAN (FDA Center for Food Safety...)
PRJNA578397	Contigs	Campylobacter sp.	GenomeTrakr Project: Kentucky Department for Public Health (FDA Center for Food Safety...)
PRJNA675633	Contigs	Campylobacter sp.	GenomeTrakr Project: Michigan Department of Health and Human Services (Michigan Department of Health...)
PRJNA675645	No data links	Campylobacter sp.	GenomeTrakr Project: VT Dept. of Health, Campylobacter sp. (Vermont Department of Health...)
PRJNA763586	Contigs	Campylobacter sp.	Genome Trakr Project: Rhode Island Department of Health (Rhode Island State Health...)
PRJNA788759	Contigs	Campylobacter sp.	GenomeTrakr Project: New York State Department of Agriculture and Markets (NYAG) (GenomeTrakr Project: New...)
PRJNA984751	Contigs	Campylobacter sp.	GenomeTrakr Project: AZ State Public Health, TGen North -- Campylobacter sp. (AZ GenomeTrakr submission...)
PRJNA1005262	SRA or Trace	Campylobacter sp.	GenomeTrakr Project: SDSU Veterinary & Biomedical Sciences/ DOH South Dakota (GenomeTrakr Project: SDSU...)
PRJNA1011942	Contigs	Campylobacter sp.	Campylobacter sp. SENASICA MX (SENASICA)

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Campylobacter

GenomeTrakr umbrella project for Campylobacter jejuni and Campylobacter coli

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