cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000561
title: Investigating the diversity of Vibrio cholerae isolates

description: BACKGROUND: Cholera is endemic in Bangladesh, with outbreaks reported annually. Currently, the majority of epidemic cholera reported globally is El Tor biotype Vibrio cholerae isolates of the serogroup O1. However, in Bangladesh, outbreaks attributed to V. cholerae serogroup O139 isolates, which fall within the same phylogenetic lineage as the O1 serogroup isolates, were seen between 1992 and 1993 and in 2002 to 2005. Since then, V. cholerae serogroup O139 has only been sporadically isolated in Bangladesh and is now rarely isolated elsewhere. METHODS: Here, we present case histories of four cholera patients infected with V. cholerae serogroup O139 in 2013 and 2014 in Bangladesh. We comprehensively typed these isolates using conventional approaches, as well as by whole genome sequencing. Phenotypic typing and PCR confirmed all four isolates belonging to the O139 serogroup. FINDINGS: Whole genome sequencing revealed that three of the isolates were phylogenetically closely related to previously sequenced El Tor biotype, pandemic 7, toxigenic V. cholerae O139 isolates originating from Bangladesh and elsewhere. The fourth isolate was a non-toxigenic V. cholerae that, by conventional approaches, typed as O139 serogroup but was genetically divergent from previously sequenced pandemic 7 V. cholerae lineages belonging to the O139 or O1 serogroups. CONCLUSION: These results suggest that previously observed lineages of V. cholerae O139 persist in Bangladesh and can cause clinical disease and that a novel disease-causing non-toxigenic O139 isolate also occurs. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/about/who-we-are/policies/open-access-science http://www.sanger.ac.uk/resources/downloads/bacteria/
DOI: 10.26036/cnphis0000562
title: Salmonella Typhi and Salmonella Paratyphi A Strains

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000563
title: Salmonella Paratyphi B and Java Genome Sequencing Program

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000564
title: Salmonella virchow

description: For further information on this study please see http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000565
title: Salmonella Paratyphi A global variation

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000566
title: Salmonella enterica variation

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000567
title: Salmonella enterica diversity

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0001261
title: Millepora alcicornis Genome sequencing

description: Microsatellite study. Millepora alcicornis branching type from Media Luna, La Parguera, Puerto Rico.
DOI: 10.26036/cnphis0001262
title: Haemonchus contortus genomic sequence (from McMaster)

description: Genomic sequence component of "Haemonchus contortus genome and developmental transcriptome."
DOI: 10.26036/cnphis0001263
title: Leiopathes glaberrima Genome sequencing

description: Microsatellite comparisons
DOI: 10.26036/cnphis0001264
title: Pachypsylla venusta Genome sequencing

description: Whole genome assembly of Pachypsylla venusta (Hackberry petiole gall psyllid) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001265
title: Corynactis californica Genome sequencing

description: Microsatellite characterization
DOI: 10.26036/cnphis0001266
title: Amplexidiscus fenestrafer Genome sequencing

description: Microsatellite characterization
DOI: 10.26036/cnphis0001267
title: Anoplophora glabripennis isolate:ALB-LARVAE Genome sequencing

description: Whole genome assembly of Anoplophora glabripennis (Asian long-horned beetle) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001268
title: Fasciolopsis buski Transcriptome or Gene expression

description: Fasciolopsis buski is a socioeconomically important and one of the largest intestinal flukes of pigs and humans with a flat and thick body of 2-10 cm in length and 0.8-3 cm in width that causes the disease fasciolopsiasis. The infective cysted stages of this flatworm develop on the surface of aquatic plants, eg. Water caltrop and reach their host due to ingestion of such contaminated vegetation. In several countries, this neglected tropical disease is aggravated by factors, such as poverty, malnutrition, and an uncontrolled food market associated with lack of food inspection, poor sanitation, and other helminthiases. Although fasciolopsiasis can be controlled along with other food-borne parasitoses, it still remains a public health problem in many endemic areas including India despite sustained WHO control programmes. The parasite is a close relative of liver flukes (Fasciola). Very little is known about this parasite and its relationship with its hosts at the molecular level. Here, we carried out advanced sequencing and bioinformatic technologies employed to explore the genes transcribed in the adult stage of F. buski.
DOI: 10.26036/cnphis0001943
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001944
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001945
title: Ophiothrix spiculata isolate:Osp01 Variation

description: Whole genome assembly and analysis of Ophiothrix spiculata using multiple sequencing technologies.
DOI: 10.26036/cnphis0001946
title: Zonotrichia albicollis isolate:Tan morph Genome sequencing and assembly

description: The White-throated Sparrow is a passerine bird of the American sparrow family Emberizidae, which has been studied extensively as it maintains a 100Mb inversion polymorphism on chromosome 2 via disassortative mating. The inverted arrangement is maintained in a near constant state of heterozygosity. Approximately half of the population is homozygous for the ZAL2 arrangement, whereas the other half of the population has the heterozygous condition. The exceptional inversion polymorphism (ZAL2m) in the white-throated sparrow (Zonotrichia albicollis) is linked to variation in plumage, social behavior and mate choice, and is maintained in the population by negative assortative mating.
DOI: 10.26036/cnphis0001947
title: RNA-Seq studies identify cancer-related genes differentially regulated during inflammation-driven lung tumorigenesis and modulated by chemopreventive agents

description: Purpose: Chronic pulmonary inflammation in the form of chronic obstructive pulmonary disease (COPD) has been consistently shown to increase the risk of lung cancer. Therefore, identification of chemopreventive agents with anti-inflammatory effects, in addition to antiproliferative and apoptotic activities, is indispensable. Recently, we found that combinations of silibinin (Sil) and indole-3-carbinol (I3C) significantly inhibited lung tumorigenesis induced by 4-(methylnitro-samino)-1-(3-pyridyl)-1-butanone (NNK) and enhanced by chronic treatment with the inflammatory agent lipopolysaccharide (LPS). In this study, we described gene expression profiling of lung tissues using RNA-seq to determine the gene expression signature in inflammation-driven lung tumors and modulation of this signature by the chemopreventive agents Sil and I3C. Methods: Total RNA extracted from lung tissues of control and treated mice were processed for mRNA sequencing, in triplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed for transcript abundance at the gene level using CLC Bio Genomics Workbench and differential gene expression analysis was performed using the built-in Empirical Analysis of Differential Gene Expression (DGE) based on ''Exact Test'' method. qRT–PCR validation was performed using SYBR Green assays. Results and conclusions: We found that 330, 2,957, and 1,143 genes were differentially regulated in mice treated with NNK, LPS, and NNK + LPS, respectively. The expression of inflammation-and immunity-related genes was significantly more deregulated in lung tissues of mice treated with LPS alone compared to mice treated with NNK + LPS. Among 1,143 genes differentially regulated in the NNK + LPS group, the expression of 162 genes and associated signaling pathways were significantly modulated by I3C and/or Sil + I3C. These genes include cytokines, chemokines, and genes with a well-established role in inflammation and/or tumorigenesis such as c-ros oncogene 1 (Ros1), the EGFR ligands amphiregulin and epiregulin, Cyp1a1, and the circadian rhythm genes Arntl, and Npas2. To our knowledge, this is the first report that provides insight into genes that are differentially expressed during inflammation-driven lung tumorigenesis and the modulation of these genes by chemopreventive agents. Overall design: Lung tissue mRNA profiles of mice treated with control vehicle, NNK, LPS, NNK+LPS, or NNK+LPS supplemented with chemopreventive agent(s) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.
DOI: 10.26036/cnphis0001948
title: Dreissena polymorpha isolate:RR_01 Genome sequencing and assembly

description: Markers isolation
DOI: 10.26036/cnphis0001949
title: Biomphalaria glabrata 13-16-R1 inbred lines

description: Inbred lines of the snail Biomphalaria glabrata developed from the 13-16-R1 strain, for the purpose of studying immunity to the parasite Schistosoma mansoni.
DOI: 10.26036/cnphis0001950
title: Toxocara canis isolate:PN_DK_2014 Genome sequencing

description: Genome of Toxocara canis.
DOI: 10.26036/cnphis0001952
title: Conus consors Genome sequencing

description: Sequencing of the genome of the Conus consors
DOI: 10.26036/cnphis0000568
title: Salmonella_Typhi_fluoroquinolone_resistance_study

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000569
title: Salmonella_Typhi_and_Salmonella_Paratyphi_A_Strains_II

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000570
title: Blautia_producta_genpme_comparisons

description: http://www.sanger.ac.uk/resources/downloads/bacteria/
DOI: 10.26036/cnphis0000571
title: Characterisation of the phylogenetic relationship of Salmonella enterica subsp. enterica (Subspecies I) Serotype 4,[5],12:i:-

description: Microevolution associated with emergence and expansion of new epidemic clones of bacterial pathogens holds the key to epidemiologic success. To determine microevolution associated with monophasic Salmonella Typhimurium during an epidemic, we performed comparative whole-genome sequencing and phylogenomic analysis of isolates from the United Kingdom and Italy during 2005-2012. These isolates formed a single clade distinct from recent monophasic epidemic clones previously described from North America and Spain. The UK monophasic epidemic clones showed a novel genomic island encoding resistance to heavy metals and a composite transposon encoding antimicrobial drug resistance genes not present in other Salmonella Typhimurium isolates, which may have contributed to epidemiologic success. A remarkable amount of genotypic variation accumulated during clonal expansion that occurred during the epidemic, including multiple independent acquisitions of a novel prophage carrying the sopE gene and multiple deletion events affecting the phase II flagellin locus. This high level of microevolution may affect antigenicity, pathogenicity, and transmission. http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000572
title: Illumina bodyMap2 transcriptome

description: None
DOI: 10.26036/cnphis0000573
title: Genetic diversity in Staphylococcus aureus (European collection)

description: The implementation of routine whole-genome sequencing (WGS) promises to transform our ability to monitor the emergence and spread of bacterial pathogens. Here we combined WGS data from 308 invasive Staphylococcus aureus isolates corresponding to a pan-European population snapshot, with epidemiological and resistance data. Geospatial visualization of the data is made possible by a generic software tool designed for public health purposes that is available at the project URL (http://www.microreact.org/project/EkUvg9uY?tt=rc). Our analysis demonstrates that high-risk clones can be identified on the basis of population level properties such as clonal relatedness, abundance, and spatial structuring and by inferring virulence and resistance properties on the basis of gene content. We also show that in silico predictions of antibiotic resistance profiles are at least as reliable as phenotypic testing. We argue that this work provides a comprehensive road map illustrating the three vital components for future molecular epidemiological surveillance: (i) large-scale structured surveys, (ii) WGS, and (iii) community-oriented database infrastructure and analysis tools. http://www.sanger.ac.uk/resources/downloads/bacteria/staphylococcus-aureus.html
DOI: 10.26036/cnphis0000574
title: Genomic_variation_in_a_global_set_of_Salmonella_Paratyphi_A_isolates

description: Salmonella Paratyphi A is the causative agent of paratyphoid fever, a disease virtually indistinguishable from typhoid fever. Over the past decade the incidence of paratyphoid fever caused by Salmonella Paratyphi A has increased dramatically, and in some areas has surpassed typhoid fever incidence. Salmonella Paratyphi A is genetically monomorphic, with the first two finished genome sequences differing by fewer than 200 single nucleotide polymorphisms and very few insertions or deletions. Very few molecular typing tools are able to differentiate among Salmonella Paratyphi A isolates at all, with phage typing, ribotyping and PFGE showing limited discriminatory power. In order to identify sequence polymorphisms within the global Salmonella Paratyphi A population, a total of 155 novel isolates of Paratyphi A were assembled for whole genome sequencing using multiplex Illumina/Solexa sequencing. http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000575
title: Salmonella_Dublin_genome_assembly

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000576
title: Salmonella typhimurium (tropical isolates)

description: Two lineages of Salmonella enterica serovar Typhimurium (S. Typhimurium) of multi-locus sequence type ST313 have been linked with the emergence of invasive Salmonella disease across sub-Saharan Africa. The expansion of these lineages has a temporal association with the HIV pandemic and antibiotic usage. We analysed the whole genome sequence of 129 ST313 isolates representative of the two lineages and found evidence of lineage-specific genome degradation, with some similarities to that observed in S. Typhi. Individual ST313 S. Typhimurium isolates exhibit a distinct metabolic signature and modified enteropathogenesis in both a murine and cattle model of colitis, compared to S. Typhimurium outside of the ST313 lineages. These data define phenotypes that distinguish ST313 isolates from other S. Typhimurium and may represent adaptation to a distinct pathogenesis and lifestyle linked to an-immuno-compromised human population. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/about/who-we-are/policies/open-access-science http://www.sanger.ac.uk/resources/downloads/bacteria/
DOI: 10.26036/cnphis0001269
title: Eunicea flexuosa Genome sequencing

description: Microsatellite characterization
DOI: 10.26036/cnphis0001270
title: Plumarella sp. DR-2012 Genome sequencing

description: Microsatellite characterization
DOI: 10.26036/cnphis0001271
title: Limnephilus lunatus Genome sequencing and assembly

description: Whole genome assembly of Caddis fly (Limnephilus lunatus) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0001272
title: Homalodisca vitripennis Genome sequencing

description: Whole genome assembly of Glassy-winged sharpshooter (Homalodisca vitripennis) as part of the BCM-HGSC i5k Pilot Project
DOI: 10.26036/cnphis0001273
title: Homo sapiens Genome sequencing

description: SK-BR-3 sequencing data for BreakTrans
DOI: 10.26036/cnphis0001274
title: Salmonella enterica subsp. enterica serovar Newport str. USMARC-S3124.1 Genome sequencing

description: This serovar is an important foodborne pathogen that causes disease in humans and cattle. Isolates are frequently observed to be resistant to multiple antimicrobial agents. This strain will be used for comparative analysis.
DOI: 10.26036/cnphis0001275
title: Metridium senile Genome sequencing

description: Microsatellite characterization of Metridium senile from aquarium.
DOI: 10.26036/cnphis0001276
title: Tanacetipathes sp. 09_290 Genome sequencing

description: microsatellite characterization
DOI: 10.26036/cnphis0001277
title: GenomeTrakr Project: Washington State Department of Health Public Health Laboratory

description: Currently encompasses whole genome sequencing of cultured pathogens as part of a surveillance project for the rapid detection of outbreaks of foodborne illnesses
DOI: 10.26036/cnphis0001951
title: Papilio glaucus Genome sequencing and assembly

description: de novo genome sequencing of Papilio glaucus
DOI: 10.26036/cnphis0001953
title: Macoma balthica Mitogenome sequencing

description: None
DOI: 10.26036/cnphis0001954
title: Hawaiian Honeycreeper Genome Sequencing

description: Hawaiian honeycreepers are an avian adaptive radiation including many endangered and extinct species. They are a model system for study of evolution, disease resistance, and other topics. The goal of this study is to provide a genome sequence and related resources (SNPs) for Hawaiian honeycreepers.
DOI: 10.26036/cnphis0001955
title: Miniopterus natalensis Epigenomics

description: Identify potential active or repressed enhancers in bat developing bat forelimbs and hindlimb. This will add in understanding of what genetic changes have allowed for the evolution of bat wings.
DOI: 10.26036/cnphis0001956
title: Nile Perch, Lates niloticus, 454 next generation sequencing

description: Development of Genome wide microsatellite genetic resources in a freshwater species, the Nile perch, Lates niloticus
DOI: 10.26036/cnphis0001957
title: Ginkgo biloba Transcriptome or Gene expression

description: The gold of this project is to identify a number of Ginkgo transcripts using de novo assenbly of next-generation sequencing
DOI: 10.26036/cnphis0001958
title: Catajapyx aquilonaris Genome sequencing

description: Whole genome assembly of Silvestris northern forceptail (Catajapyx aquilonaris) as part of the BCM-HGSC i5k Pilot Project
DOI: 10.26036/cnphis0001959
title: Ixodes ricinus strain:Charles River Genome sequencing and assembly

description: In Europe, ticks are the main vectors of human diseases and also affect livestock, wildlife and pet animals. Here we present the first study about whole genome shotgun sequencing of Ixodes ricinus, the most important European tick. High molecular weight DNA was extracted out of adult males. The v01 assembly is composed of 998,100,906 paired reads obtained from Illumina HiSeq 2000 sequencing that were de novo assembled into 235,953 contigs. The v02 assembly is composed of PacBio reads assembled into 204,516 contigs.
DOI: 10.26036/cnphis0001960
title: Stylissa carteri Genome sequencing

description: Hologenome sequencing of Red Sea sponge, Stylissa carteri
DOI: 10.26036/cnphis0000577
title: Recrudescent Salmonella study

description: "High-resolution single nucleotide polymorphism analysis distinguishes recrudescence and reinfection in recurrent invasive nontyphoidal Salmonella typhimurium disease." Pubmed ID: 22318974. Bloodstream infection with invasive nontyphoidal Salmonella (iNTS) is common and severe among human immunodeficiency virus (HIV)-infected adults throughout sub-Saharan Africa. The epidemiology of iNTS is poorly understood. Survivors frequently experience multiply recurrent iNTS disease, despite appropriate antimicrobial therapy, but recrudescence and reinfection have previously been difficult to distinguish. We used high-resolution single nucleotide polymorphism (SNP) typing and whole-genome phylogenetics to investigate 47 iNTS isolates from 14 patients with multiple recurrences following an index presentation with iNTS disease in Blantyre, Malawi. We isolated nontyphoidal salmonellae organisms from blood (n = 35), bone marrow (n = 8), stool (n = 2), urine (n = 1), and throat (n = 1) samples; these isolates comprised serotypes Typhimurium (n = 43) and Enteritidis (n = 4). Recrudescence with identical or highly phylogenetically related isolates accounted for 78% of recurrences, and reinfection with phylogenetically distinct isolates accounted for 22% of recurrences. Both recrudescence and reinfection could occur in the same individual, and reinfection could either precede or follow recrudescence. The number of days to recurrence (23-486 d) was not different for recrudescence or reinfection. The number of days to recrudescence was unrelated to the number of SNPs accumulated by recrudescent organisms, suggesting that there was little genetic change during persistence in the host, despite exposure to multiple courses of antibiotics. Of Salmonella Typhimurium isolates, 42 of 43 were pathovar ST313. High-resolution whole-genome phylogenetics successfully discriminated recrudescent iNTS from reinfection, despite a high level of clonality within and among individuals, giving insights into pathogenesis and management. These methods also have adequate resolution to investigate the epidemiology and transmission of this important African pathogen. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/about/who-we-are/policies/open-access-science http://www.sanger.ac.uk/resources/downloads/bacteria/
DOI: 10.26036/cnphis0000578
title: Discovery_of_sequence_diversity_in_Staphylococcus_aureus_ST22_and_ST36

description: http://www.sanger.ac.uk/resources/downloads/bacteria/staphylococcus-aureus.html