cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000645
title: Genomic characterization of SPI-1 lacking Salmonella Senftenberg isolates from China.

description: Infections associated with Salmonella enterica subspecies enterica serovar Senftenberg are often associated with poultry flocks, farm environments, and consumption of mussels and vegetables as sources. The recent emergence of multidrug resistant isolates, both in Africa and the United States, has raised public health concerns. In this study comparative genomic analysis and phenotyping were used to characterize 14 clinical Salmonella Senftenberg isolates recovered from Shenzhen and Shanghai, China between 2002 and 2011.All S. Seftenberg isolates (except S10078 and S11192) were previously characterized by deletion of Salmonella Pathogenicity Island 1. DNA prepared from all isolates was sequenced using an Illumina HiSeq platform and Multilocus Sequencing Type (MLST), antimicrobial profiles, single nucleotide polymorphisms (SNPs), genome architecture and protein families were determined. SNP analyses indicated that the studied S. Senftenberg isolates belonged to two distinct phylogenetic clades designated SC1&SC2 that were distinguished in the genomic architecture, invasion capability and abundance of protein families.
DOI: 10.26036/cnphis0000646
title: The initial state of the human gut microbiome determines its reshaping by antibiotics

description: The human gut microbiota is affected by antibiotics, but the heterogeneous response between individuals remains unexplored. To specifically address this question and examine the effect of antibiotics on selection of resistance genes, we administered the second-generation cephalosporin cefprozil to healthy volunteers. Stool samples gathered before antibiotic exposure, at the end of the treatment and three months later were analyzed using shotgun metagenomic sequencing. We show that normal antibiotic treatment can alter the gut microbiome in a specific, reproducible and predictable fashion. Strikingly, we identified a subgroup of participants that were enriched in opportunistic pathogen Enterobacter cloacae after exposure to the antibiotic, an effect linked to lower initial microbiome diversity and to the Bacteroides enterotype. Resistance genes that were not detectable before the treatment were observed after a 7-day course of antibiotic. Knowledge of the initial composition of the microbiome could assist in the prevention of the adverse effects of antibiotics.
DOI: 10.26036/cnphis0001342
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001343
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001344
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001345
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001346
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001347
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001348
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001349
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002025
title: Antimicrobial Surveillance from Brigham & Women''s Hospital, Boston MA

description: The goal of this project is to identify carbapenemases and other beta-lactamases in clinical isolates with WGS and assess their mobilization potential . The results can support national surveillance of clinically identified pathogens and provide invaluable information to infection control in hospital.
DOI: 10.26036/cnphis0002026
title: Metagenome sequencing of the Hadza hunter-gatherer gut microbiota.

description: By human microbiome sequencing we can better understand how host evolutionary and ontogenetic history is reflected in the microbial function. However, there has been no information on the gut metagenome configuration in hunter-gatherer populations, posing a gap in our knowledge of gut microbiota (GM)-host mutualism arising from a lifestyle that describes over 90% of human evolutionary history. Here, we present the first metagenomic analysis of GM from Hadza hunter-gatherers of Tanzania, showing a unique enrichment in metabolic pathways that align with the dietary and environmental factors characteristic of their foraging lifestyle. We found that the Hadza GM is adapted for broad spectrum carbohydrate metabolism, reflecting the complex polysaccharides in their diet. Furthermore, the Hadza GM is equipped for branched-chain amino acid degradation and aromatic amino acid biosynthesis. Resistome functionality demonstrates the existence of antibiotic resistance genes in a population with little to no antibiotic exposure, indicating the ubiquitous presence of environmentally derived resistances. Our results demonstrate how the functional specificity of the GM correlates with environment and lifestyle, and how complexity from the exogenous environment is matched by endogenous homeostasis. The Hadza gut metagenome structure allows to appreciate the co-adaptive functional role of the GM in complementing the human physiology, providing a better understanding of the versatility of human life and subsistence.
DOI: 10.26036/cnphis0002027
title: Bos taurus Genome sequencing

description: Bovine introgression in Yak
DOI: 10.26036/cnphis0002028
title: Dissecting the direct reprogramming path of fibroblasts into neurons by single cell RNA-sequencing

description: Direct lineage reprogramming represents a remarkable conversion of cellular and transcriptome states. However, the intermediates through which individual cells progress are largely undefined. Here we used single cell RNA-seq at multiple time points to dissect direct reprogramming from mouse embryonic fibroblasts (MEFs) to induced neuronal (iN) cells. By deconstructing heterogeneity at each time point and ordering cells by transcriptome similarity rather than time we reconstructed a continuous reprogramming path. We find that overexpression of a single factor (Ascl1) results in a well-defined initialization causing cells to exit the cell cycle and re-focus gene expression through distinct neural transcription factors. However, overexpression of Ascl1 alone leads to abundant alternative fates that are suppressed by the combination of additional factors (Myt1l, Pou3f2). We find transgene silencing and emergence of alternative fates are the major efficiency limits of direct reprogramming. These data provide a high-resolution approach for understanding transcriptome states during lineage differentiation. Overall design: 405 single-cell transcriptomes from 5 time points (0 days, 2 days, 5 days, 20 days and 22 days upon Ascl1 induction) during reprogramming of MEFs into iN cells were analyzed in total; All single cells contain 92 external RNA spike-ins; The following single cell transcriptomes were sequenced: 73 single MEF cells (day 0, iN2), 81 single cells at day 2 (iN1), 55 single cells at day 5 (iN3), 33 single cells at day 20 (iN6) and 73 single cells at day 22 (iN7,iN8) upon Ascl1 induction from virally transfected MEFs. Additionally, we generated the transcriptome of 47 single cells that were induced with Ascl1 for 2 days from a clonal MEF line with a uniform Ascl1 transgene copy number (iN5). Finally, we sequenced the transcriptome of 43 single cells at day 22 (iN4) upon induction of Ascl1, Brn2 and Myt1l. All single cell samples were processed on the microfluidic Fluidigm C1 platform.
DOI: 10.26036/cnphis0002029
title: Apis laboriosa Genome sequencing and assembly

description: Complete mitochondrial genome of Apis laboriosa collected from Mizoram, India
DOI: 10.26036/cnphis0002030
title: Apis andreniformis Genome sequencing and assembly

description: Complete mitochondrial genome of Apis andreniformis collected from Mizoram,India
DOI: 10.26036/cnphis0002031
title: Human Microbiome Environment Metagenome

description: The samples within this Bioproject represent the third phase (Phase III) of metagenomic sequencing (whole genome shotgun (WGS) sequencing) of microbial communities from specimens collected as a part of the NIH-supported Human Microbiome Project (HMP Consortium A framework for human microbiome research. Nature. 2012 Jun 13;486(7402):215-21. doi: 10.1038/nature11209). The sample collection represents a unique reference resource of microbiome samples from healthy adults largely residing in the USA at the time of sample collection. In the HMP Phase III component the goal has been to supplement previous WGS sequencing by generating additional sequence from as many of the specimens in the HMP collection as possible that had not been sequenced in the previous HMP Phase I and Phase II sequencing. In Phase III, a focus was placed on six of the 18 body sites: Stool (gut), Buccal mucosa (oral), Supragingival plaque (oral), Tongue dorsum (oral), Anterior nares (nasal), Posterior fornix (vaginal) and the goal was to further capture as many of the longitudinal samples (second and third visits by the same individual) as possible. From genomic DNA extracted from the collected specimens, WGS sequence was produced from libraries constructed from using a NexteraXT library construction protocol. All libraries were sequenced using a 100bp paired end approach using the Illumina HiSeq 2000 platform.
DOI: 10.26036/cnphis0002032
title: Salmonella enterica subsp. enterica Genome sequencing and assembly

description: Salmonella enterica subsp. enterica Genome sequencing and assembly project
DOI: 10.26036/cnphis0002033
title: Salmonella enterica subsp. diarizonae genome sequencing, assembly and detection of variation

description: With this project the genomic variation of three Salmonella enterica subsp. diarizonae 60:r:z strains isolated from a single patient will be investigated. The genome of the first isolate will be sequenced and assembled using a combination of PacBio and Illumina (MiSeq) sequencing technology, the two subsequent isolates will be sequenced using the Illumina MiSeq only.
DOI: 10.26036/cnphis0002034
title: Equus asinus Raw sequence reads

description: De novo assemble of the donkey white blood cell transcriptome
DOI: 10.26036/cnphis0000647
title: Genetic Difference among Salmonella Typhimurium Phage Types

description: Phage typing of Salmonella Typhimurium has been used for more than four decades as a rapid, low cost approach for the epidemiological surveillance. Bacterial resistance to phages may be related to lack of suitable receptors on the bacterial surface, host restriction modification, clusters of regulatory interspaced short palindromic repeats and superinfection exclusion systems. we are investigating variation in these systems that might be associated with the evolution of the bacterial host.
DOI: 10.26036/cnphis0000648
title: Drosophila melanogaster Canton-S sub-strain genome sequencing project

description: Whole genome shotgun sequences for multiple sub-strains of the wild-type Canton-S laboratory strain of Drosophila melanogaster. Sub-strains selected for sequencing are described in: Colomb and Brembs (2014) Sub-strains of Drosophila Canton-S differ markedly in their locomotor behavior. F1000Research 3:176 (doi: 10.12688/f1000research.4263.1).
DOI: 10.26036/cnphis0000649
title: Population genomics and phylogenomics of Alcolapia

description: Genomic signature of an endemic cichlid fish adaptive radiation from an extreme lake environment
DOI: 10.26036/cnphis0000650
title: RNA sequencing of ten chicken embryo tissues in comparison to proteome mass spectrometry

description: We sequenced total mRNA from five male and five female chicken embryos for ten different tissues. The same samples were run through a tandem mass spectrometre for proteome quantification. The study aims at comparing RNA and protein levels and making inferences about gene expression regulation at the translation level.
DOI: 10.26036/cnphis0000651
title: Single-cell transcriptome sequencing from mouse mTECs

description: Promiscuous gene expression (pGE) of tissue-restricted antigens in medullary thyme ephitelial cells (mTECs) is essential for self-tolerance induction and to prevent autoimmunity. We sequenced single mTEC transcriptomes to explore gene expression heterogeneity and to discover patterns of regulation of pGE.
DOI: 10.26036/cnphis0000652
title: Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

description: OBJECTIVES: Antimicrobial susceptibility testing of bacterial isolates is essential for clinical diagnosis, to detect emerging problems and to guide empirical treatment. Current phenotypic procedures are sometimes associated with mistakes and may require further genetic testing. Whole-genome sequencing (WGS) may soon be within reach even for routine surveillance and clinical diagnostics. The aim of this study was to evaluate WGS as a routine tool for surveillance of antimicrobial resistance compared with current phenotypic procedures. METHODS: Antimicrobial susceptibility tests were performed on 200 isolates originating from Danish pigs, covering four bacterial species. Genomic DNA was purified from all isolates and sequenced as paired-end reads on the Illumina platform. The web servers ResFinder and MLST (www.genomicepidemiology.org) were used to identify acquired antimicrobial resistance genes and MLST types (where MLST stands for multilocus sequence typing). ResFinder results were compared with phenotypic antimicrobial susceptibility testing results using EUCAST epidemiological cut-off values and MLST types. RESULTS: A total of 3051 different phenotypic tests were performed; 482 led to the categorizing of isolates as resistant and 2569 as susceptible. Seven cases of disagreement between tested and predicted susceptibility were observed, six of which were related to spectinomycin resistance in Escherichia coli. Correlation between MLST type and resistance profiles was only observed in Salmonella Typhimurium, where isolates belonging to sequence type (ST) 34 were more resistant than ST19 isolates. CONCLUSIONS: High concordance (99.74%) between phenotypic and predicted antimicrobial susceptibility was observed. Thus, antimicrobial resistance testing based on WGS is an alternative to conventional phenotypic methods.
DOI: 10.26036/cnphis0000653
title: Bloodstream_surveillence_across_Africas

description: A survey across centres in Africa into the main bacterial causes of bloodstream infections.
DOI: 10.26036/cnphis0000654
title: Resequencing of Tasmanian devil genomes

description: The Tasmanian devil is currently threatened with extinction in the wild due to the transmissible cancer devil facial tumour disease. An insurance population has been established to ensure the survival of the species. We have resequenced whole genomes of 12 Tasmanian devils from a wild population that displayed lower disease prevalence including 6 devils who spontaneously recovered from the disease. We are using the genomic information to discover any genomic regions which may be associated with disease resistance in this population. We are also utilising the data as an ascertainment panel for marker discovery for development of genotyping assays for the Tasmanian devil insurance population.
DOI: 10.26036/cnphis0000655
title: Parallel_sequencing_of_single_cell_genomes_and_transcriptomes_from_mouse_8_cell_stage_embryos

description: The simultaneous sequencing of the genome and transcriptome of a single cell offers a powerful means to dissect genetic heterogeneity and its effect on gene expression. Here we describe G&T–seq, a method for separating and sequencing genomic DNA and full–length mRNA from single cells. By applying G&T–seq to over 220 single cells from mouse and human we reveal cellular properties that cannot be inferred from DNA or RNA sequencing alone. This data details the mouse 8-cell stage embryos described in the manuscript.
DOI: 10.26036/cnphis0001350
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001351
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001352
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001353
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001354
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001355
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001356
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001357
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001358
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001359
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002035
title: Genome resequencing of Old World camels

description: This study aims to sequence the genomes of multiple individuals from the three species of Old World camels (Camelus dromedarius, Camelus ferus, Camelus bactrianus). By identifying the underlying genetic variation, we can discover how domestication has shaped their genomes.
DOI: 10.26036/cnphis0002036
title: Drosophila_melanogaster_RNA_seq_Raw_reads_eclosion

description: In this study we generated RNA_seq profiles for 2 DGRP lines showing substantial difference in eclosion phase. The samples are represented by Pupae collected at 6 time points the day before eclosion. The objective is to identify transcripts and pathways associated with different Chronotypes (phase of eclosion).
DOI: 10.26036/cnphis0002037
title: Euperipatoides rowelli isolate:MRLB_TSF Genome sequencing

description: Whole genome assembly of Velvet worm (Euperipatoides rowelli) as part of the BCM-HGSC i5k Pilot Project.
DOI: 10.26036/cnphis0002038
title: Caligus rogercresseyi Genome sequencing and assembly

description: Caligus rogercresseyi has become an important model for the study of ectoparasitic infestations on salmon. The process of disease due to C. rogercresseyi on farmed Atlantic salmon (Salmo salar) in Chile is a result of their feeding behavior and the secretion of bioactive compounds into the host. Clinical signs include physical damage to the epidermis and underlying tissue, changes in the blood electrolyte composition, physiological stress, immune dysfunction, loss of locomotive capacity and sometimes, death. Susceptibility to this louse varies among the various fish species in the southern Pacific Ocean. In farming, the ectoparasite is important because of production losses and significant costs of treatment.
DOI: 10.26036/cnphis0002039
title: Lepeophtheirus salmonis Atlantic Canada genome sequencing project

description: Lepeophtheirus salmonis (Atlantic) has become an important model for the study of ectoparasitic infestations on salmon. The process of disease due to L. salmonis on Atlantic salmon (Salmo salar) and sea trout (S. trutta) is a result of their feeding behavior and the secretion of bioactive compounds into the host. Clinical signs include physical damage to the epidermis and underlying tissue, changes in the blood electrolyte composition, physiological stress, immune dysfunction, loss of locomotive capacity and sometimes, death. Innate resistance to the salmon louse varies among the various species of salmon and trout. In addition, the question arises as to whether separate Atlantic and Pacific populations of L. salmonis have co-evolved with Atlantic salmon and Pacific salmon respectively. Recent data suggests that the Pacific Ocean population may be a distinct group from the Atlantic Ocean population. The salmon louse, Lepeophtheirus salmonis, is a common parasite of the skin of farmed and wild salmon throughout the northern hemisphere. In farming, the parasite is important because of production losses and significant costs of treatment. Furthermore, the salmon louse is notable for the debates that disease is transmitted between farmed and iconic wild salmon populations.
DOI: 10.26036/cnphis0002040
title: Fasciola gigantica Genome sequencing

description: Fasciola gigantica is a parasitic flatworm of the class Trematoda, which causes tropical fascioliasis. It is regarded as one of the most important single platyhelminth infections of ruminants in Asia and Africa. Estimates of infection rates are as high as 80-100% in some countries. The infection is commonly called fasciolosis. The prevalence of F. gigantica often overlaps with that of Fasciola hepatica, and the two species are so closely related in terms of genetics, behaviour, and morphological and anatomical structures that it is notoriously difficult to distinguish them. Therefore, sophisticated molecular techniques are required to correctly identify and diagnose the infection.
DOI: 10.26036/cnphis0002041
title: GenomeTrakr Project: UCD Centre for Food Safety

description: Microbial foodborne pathogens sequenced for the UCD Centre for Food Safety Genome sequencing
DOI: 10.26036/cnphis0002042
title: Whole genome sequencing of two Ammodramus sparrows

description: The goal of this study was the development of diagnostic microsatellite loci in two hybridizing congeneric sparrow species.
DOI: 10.26036/cnphis0000656
title: Salmonella_surveillance_study

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000657
title: A novel KIT variant in an Icelandic horse with white spotted coat colour

description: Background: Variants in the KIT gene are responsible for completely white or white spotting phenotypes in many different species. To the authors’ knowledge there are currently 22 defined equine KIT variants that lead to a reduced number of melanocytes. The resulting coat colour phenotypes range from the completely dominant white horses to just a slight increase in the quantitative trait white markings. The known equine KIT variants are responsible for the allele series termed W1 to W201-5, in addition to the sabino-1 (SB1)6 and tobiano (TO)7 alleles. Own analysis: We sequenced the genome of an Icelandic horse with a striking white spotted phenotype (Fig. 1). The horse was born out of solid-coloured parents. We obtained xxx 2 x 125 bp read-pairs on an illumina Hiseq2500, of which yyy read-(pairs) mapped to the EquCab 2 reference genome yielding an 11.1x average genome coverage. The sequence data were submitted to the European Nucleotide Archive with the accession number ????. We analysed the genome sequence for coding variants in the functional candidate genes EDNRB8, KIT, MITF9, and PAX35,9 (Table S1). The horse did not carry any obvious functional variants in EDNRB, MITF, or PAX3. However, we noticed a heterozygous deletion of a single nucleotide in exon 17 of the KIT gene (chr3:77,735,488delG, c.2369delC, p.A790Efs*20). This frameshift variant is predicted to result in either nonsense mediated decay of the mutant transcript or the expression of a KIT protein with a truncated intracellular tyrosine kinase domain. We confirmed this variant by Sanger sequencing.
DOI: 10.26036/cnphis0000658
title: Exome and Whole Genome Sequencing of Single Adipocytes and Whole Blood DNA

description: Because human white adipocytes display a high turnover throughout adulthood, a continuous supply of precursor cells is required to maintain adipogenesis. Bone marrow-derived progenitor cells may contribute to mammalian adipogenesis, however results in animal models have been conflicting. We performed exome and whole genome sequencing of whole genome amplified single adipocytes from 3 subjects who previously underwent allogeneic bone marrow or peripheral blood stem cell transplantation. These individuals received donor cells that can be distiguished from recipient cells by specific polymorphic markers in the DNA. Exome- and whole genome sequencing of single adipocytes suggests that bone marrow- or peripheral stem cell derived progenitor cells contribute to adipose tissue via either differentiation or cell fusion.