cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000659
title: We carried out genomic analysis isolated in an outbreak caused by Salmonella Paratyphi A

description: An parathyroid fever outbreak was detected in Yunnan, China. We performed whole genome sequencing to track the transmission of this outbreak.
DOI: 10.26036/cnphis0000660
title: Microevolution_of_Salmonella_Paratyphi_A_during_human_infection

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000661
title: RNA-seq of gastric biopsies from subjects at different stages of gastric inflammation and histological changes.

description: In this study we performed RNA-seq analysis of gastric corpus biopsies to study transcriptional changes during early gastric carcinogenesis. We included patients with non-atrophic gastritis, with intermediate and extensive corpus atrophy, and patients with intestinal metaplasia. We also included a control group of H. pylori-negative subjects. All subjects were from Nicaragua, which has a population of high gastric cancer risk. Total RNA samples were treated with RiboZero Magnetic (Human/Mouse/Rat) Kit (Epicentre Biotechnologies) to deplete rRNA and the cDNA libraries were prepared using ScriptSeqTM v2 RNA-Seq Library Preparation Kit (Epicentre). Sequencing was performed on the Illumina HiScan2500 platform, 2*100bp reads.
DOI: 10.26036/cnphis0000662
title: Whole genome detection of sequences of six horses from diverse breeds.

description: Completed in 2009, the reference genome assembly of the domesticated horse (EquCab 2.0) produced the majority of publically available annotations of genetic variations in this species. Following that effort, a few other projects that focused at variant discovery of a particular breed or two. In this project we aim to identify and annotate single nucleotide polymorphisms (SNPs), insertions and deletions (INDELs), copy number variations (CNVs) and structural variations (SVs) in the genomes six horses of diverse genetic background using next generation sequencing.
DOI: 10.26036/cnphis0000663
title: Virulence characterisation of Salmonella enterica by a new microarray: detection and evaluation of the cytolethal distending taxin gene activity in the unusal host S, Typhimurium

description: Salmonella enterica is a zoonotic foodborne pathogen that causes acute gastroenteritis in humans. We assessed the virulence potential of one-hundred and six Salmonella strains isolated from food animals and products. A high through-put virulence genes microarray demonstrated Salmonella Pathogenicity Islands (SPI) and adherence genes were highly conserved, while prophages and virulence plasmid genes were variably present. Isolates were grouped by serotype, and virulence plasmids separated S. Typhimurium in two clusters. Atypical microarray results lead to whole genome sequencing (WGS) of S. Infantis Sal147, which identified deletion of thirty-eight SPI-1 genes. Sal147 was unable to invade HeLa cells and showed reduced mortality in Galleria mellonella infection model, in comparison to a SPI-1 harbouring S. Infantis. Microarray and WGS of S. Typhimurium Sal199, established for the first time in S. Typhimurium presence of cdtB and other Typhi-related genes. Characterization of Sal199 showed cdtB genes were upstream of transposase IS911, and co-expressed with other Typhi-related genes. Cell cycle arrest, cytoplasmic distension, and nuclear enlargement were detected in HeLa cells infected by Sal199, but not with S. Typhimurium LT2. Increased mortality of Galleria was detected on infection with Sal199 compared to LT2.
DOI: 10.26036/cnphis0000664
title: Sequencing_Salmonella_Typhi_strain

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0001360
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001361
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001362
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001363
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001364
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001365
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001366
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002043
title: Neodiprion lecontei Genome sequencing and assembly

description: Neodiprion lecontei is a relative host generalist that feeds on multiple pine tree species in North America. Study goals include genome-wide comparisons to closely related host specialists that utilize a narrower host range. Data users are expected to allow the data producers to publish the first paper with global analyses of the data, including (but not limited to) sequence data, population genetics, signals of selection, and functional annotations.
DOI: 10.26036/cnphis0002044
title: Salmonella enterica subsp. enterica serovar Derby strain:07CR553 Genome sequencing

description: None
DOI: 10.26036/cnphis0002045
title: Total RNA Sequencing of Drosophila pseudoobscura, Drosophila sechellia, Drosophila simulans, Drosophila virilis, and Drosophila yakuba transcriptome

description: Drosophila pseudoobscura, Drosophila sechellia, Drosophila simulans, Drosophila virilis, and Drosophila yakuba
DOI: 10.26036/cnphis0002046
title: Salmonella enterica subsp. enterica serovar Dublin str. SA20093032 Genome sequencing and assembly

description: Genome sequence of Salmonella enterica (serogroup D; 1,9,12:g,m,p:-)
DOI: 10.26036/cnphis0002047
title: Salmonella enterica serovar Typhimurium genome sequencing
DOI: 10.26036/cnphis0002048
title: Lates calcarifer Genome sequencing and assembly
DOI: 10.26036/cnphis0002049
title: Homo sapiens Exome
DOI: 10.26036/cnphis0002050
title: Chorthippus parallelus parallelus raw sequence reads
DOI: 10.26036/cnphis0002051
title: Salmonella enterica subsp. enterica serovar Berta str. SA20103550 Genome sequencing and assembly

description: Genome sequence of Salmonella Enteritidis (serogroup D; 1,9,12:f,g,m,t:-)
DOI: 10.26036/cnphis0002052
title: Salmonella enterica subsp. enterica serovar Gaminara str. SA20063285 Genome sequencing and assembly

description: Genome sequence of Salmonella Gaminara (serogroup I; 16:d:1,7)
DOI: 10.26036/cnphis0000665
title: Characterization of maize B73 transcriptome by hybrid sequencing

description: Zea mays is a leading model for elucidating transcriptional networks in plants, aided by increasingly refined studies of the transcriptome atlas across spatio-temporal, developmental, and environmental dimensions. Limiting this progress are uncertainties about the complete structure mRNA transcripts, particularly with respect to alternatively spliced isoforms. Although second-generation RNA-seq provides a quantitative assay for transcriptional and posttranscriptional events, the accurate reconstruction of full-length mRNA isoforms is challenging with short-read technologies. By producing much longer reads, third generation sequencing offers to solve the assembly problem, but can suffer from lower read accuracy and throughput. Here, we combine these complementary technologies to define and quantify high-confidence transcript isoforms in maize. Six tissues (root, pollen, embryo, endosperm, immature ear, and immature tassel) of the B73 inbred line were used for mRNA sequencing with the Illumina Hiseq2000 PE101 platform to comprehensively quantitate gene/isoform expression. In parallel, intact cDNAs from the same samples were sequenced using the PacBio RS II platform. The latter used four size fractionated libraries (1-2kb, 2-3kb, 3kb-5kb, 5kb-10kb) to generate more than 2 million full length reads. Preliminary findings suggest that mechanisms of alternative splicing are differentially employed between different tissues. In addition, these data show promise to dramatically improve the status of maize genome annotation, with the detection of previously unidentified transcript isoforms, and uncovering previously unrecognized genes. This submission is data of Illumina Hiseq2000 PE101 reads.
DOI: 10.26036/cnphis0000666
title: Emergence of a clonal lineage of multidrug-resistant ESBL-producing Salmonella Infantis transmitted from broilers and broiler meat to humans in Italy during the period of 2011-2014.

description: We report the spread in the Italian broiler chicken industry of a clone of multidrug-resistant (MDR), ESBL-producing (blaCTX-M-1) Salmonella enterica subsp. enterica serovar Infantis, firstly detected in Italy 2011 and causing clinical cases in 2013-2014. A set of n=49 of extended-spectrum cephalosporin (ESC)-resistant (R) isolates S. Infantis (2011-2014) from humans, food-producing animals and meat thereof were studied along a selected set of n=42 ESC-susceptible (ESC-S) isolates (2001-2014): they were characterized by macrorestriction-PFGE analysis and genetic environment of ESC-resistance. Isolates representative of PFGE-patterns and origin were submitted to Whole Genome Sequencing. The emerging ESC-R clone, detected mainly in broiler chickens, broiler meat and humans also showed ciprofloxacin microbiological resistance (MIC 0.25 mg/L) and harboured a conjugative megaplasmid (approx. 280-320 Kb, pESI-like), similar to that described in ESC-S S. Infantis in Israel in 2014. This megaplasmid carried the ESBL gene blaCTX-M-1 and further genes (tet(A), sul1, dfrA1 and dfrA14) mediating a minimum resistance pattern of cefotaxime, tetracycline, sulfonamides, and trimethoprim clinical resistance, beside genes conferring enhanced attitudes to colonization, virulence (fimbriae, yersiniabactin), resistance and fitness (qacEΔ1, mer operon) in the intensive-farming environment. Further spread of this emerging MDR, ESBL-producing S. Infantis clone in primary productions deserves quick and thorough risk-management strategies.
DOI: 10.26036/cnphis0000667
title: Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to arctic environments

description: Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below -70°C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformations, extremely hairy winter coats and acute seasonal differences in metabolic activities. The evolutionary origins of Yakutian horses and the genetic basis of their adaptations remain, however, contentious. Here we present the complete genomes of nine present-day Yakutian horses and two ancient specimens dating to the early 19th century AD and ~5,200 years ago. By comparing these to the genomes of two Late Pleistocene, 27 domesticated and three wild Przewalski’s horses, we find that contemporary Yakutian horses do not descend from the native horses that populated the region until the mid-Holocene, but were most likely introduced following the migration of the Yakut people a few centuries ago. They, thus, represent one of the fastest cases of adaptation to the extreme temperatures of the Arctic. We find cis-regulatory mutations to have contributed more than non-synonymous changes to their adaptation, likely due to the comparatively limited standing variation within gene bodies at the time the population was founded. Genes involved in hair development, body size, metabolic and hormone signaling pathways represent an essential part of the Yakutian horse adaptive genetic toolkit. Finally, we find evidence for convergent evolution with native human populations and woolly mammoths, suggesting that only a few evolutionary strategies are compatible with survival in extremely cold environments.
DOI: 10.26036/cnphis0000668
title: Molecular_epidemiology_of_ciprofloxacine_resistance_Salmonella_Typhi_in_Nepal

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000669
title: Global genomic epidemiology of Salmonella Typhimurium DT104

description: It has been 30 years since the initial emergence and subsequent rapid global spread of multidrug-resistant S. Typhimurium DT104. Nonetheless, its origin and transmission route have never been revealed. We used whole genome sequence (WGS) and temporally structured sequence analysis within a Bayesian framework to reconstruct temporal and spatial phylogenetic trees and estimate the rate of mutation and divergence time of 315 S. Typhimurium DT104 isolates sampled from 1969 to 2012 from 21 countries on six continents. DT104 was estimated to have emerged initially as antimicrobial-susceptible strains in ~1948 (95% credible interval, 1934 - 1962) and later became multidrug-resistant (MDR) DT104 in ~1972 (95% CI 1972 – 1988) through horizontal transfer of the 13-kb SGI1 MDR region into already SGI1-containing susceptible strains. This was followed by multiple transmission events initially from Central Europe and later between several European countries. An independent transmission occurred to the United States and another to Japan and from here likely to Taiwan and Canada. An independent acquisition of resistance genes took place in Thailand in ~1975 (95% CI 1975-1990). Locally in Denmark, WGS was capable of confirming local epidemiology for transmission between animal herds. Interestingly, the demographic history of Danish MDR DT104 provided evidence for the accomplishment of an eradication program across pig herds in Denmark from 1996 to 2000. The results from this study refute several hypotheses on the evolution of DT104 and would suggest WGS may be useful in monitoring emerging clones and making strategies for prevention.
DOI: 10.26036/cnphis0000670
title: Single-cell RNA-seq reveal lineage formation and X-chromosome dosage compensation in human preimplantation embryos

description: Single-cell RNA-seq of 1,469 cells obtained from 79 human preimplantation embryos ranging from embryonic day 3 to 7.
DOI: 10.26036/cnphis0000671
title: Analysis of single CD41 cell transcriptomes from Zebrafish

description: Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes, and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.
DOI: 10.26036/cnphis0000672
title: Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia

description: Inhabitants of Túquerres in the Colombian Andes have a 25-fold higher risk of gastric cancer than inhabitants of the coastal town Tumaco, despite similar H. pylori prevalences. The gastric microbiota was recently shown in animal models to accelerate the development of H. pylori-induced precancerous lesions. 20 individuals from each town, matched for age and sex, were selected, and gastric microbiota analyses were performed by deep sequencing of amplified 16S rDNA. In parallel, H. pylori status, carriage of the cag pathogenicity island and assignment of H. pylori to phylogeographic groups was performed to test for correlations between H. pylori strain properties and microbiota composition. The gastric microbiota composition was highly variable between individuals, but showed a significant correlation with the town of origin. Multiple OTUs were detected exclusively in either Tumaco or Túquerres. Two operational taxonomic units (OTUs), Leptotrichia wadei and a Veillonella sp., were significantly more abundant in Túquerres, and 16 OTUs, including a Staphylococcus sp. were significantly more abundant in Tumaco. There was no significant correlation of H. pylori phylogeographic population or carriage of the cagPAI with microbiota composition. From these data, testable hypotheses can be generated and examined in suitable animal models and prospective clinical trials.
DOI: 10.26036/cnphis0000673
title: Genomic analysis of Salmonella enterica serotype Paratyphi A during an outbreak in Cambodia, 2013-2015

description: In 2013, an unusual increase in the number of Salmonella enterica serotype Paratyphi A (Salmonella Paratyphi A) infections was reported in patients in Phnom Penh, Cambodia, and in European, American and Japanese travellers returning from Cambodia. Epidemiological investigations failed to identify a common source of exposure. Whole-genome sequencing was performed on 65 Salmonella Paratyphi A isolates: 48 from infections acquired in Cambodia between 1999 and 2014 (in both local residents and travellers) and 17 from infections acquired in other countries in Asia, Africa and Europe between 2002 and 2014. Short-read sequences from 80 published Salmonella Paratyphi A genomes from around the world and from 13 published Salmonella Paratyphi genomes associated with an outbreak in China were included in the study. Pulsed-field gel electrophoresis was performed on a subset of the isolates. All but four of the 47 isolates acquired in Cambodia between 2010 and 2014 belonged to the same clade, C5, of lineage C. This clade has been isolated in Cambodia since at least 1999. The Cambodian outbreak clade isolates displayed pan-susceptibility to antibiotics. Only one C5 isolate, collected in 2000, was resistant to quinolone and was found to carry a gyrA mutation (Ser83Phe). The Cambodian outbreak strain was different from that responsible for an outbreak in China in 2010–2011 (clade C4). Pan-genome analysis revealed no gains of particular accessory genes or losses of common genes in the C5 clade that might account for a possible selective advantage. Environmental and/or human behavioural factors are, therefore, likely to explain the recent increase in the incidence of Salmonella Paratyphi A infections in Cambodia.
DOI: 10.26036/cnphis0001367
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001368
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001369
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001370
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001371
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001372
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001373
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001374
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001375
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001376
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002053
title: Salmonella enterica subsp. enterica serovar Hadar str. SA20026260 Genome sequencing and assembly

description: Genome sequence of Salmonella Hadar (serogroup C2; 6,8:z10:e,n,x)
DOI: 10.26036/cnphis0002055
title: Phlebotomus bergeroti genome sequencing

description: Proposal for Sequencing the Genome of the Sand Flies, Lutzomyia longipalpis and Phlebotomus papatasi
DOI: 10.26036/cnphis0002056
title: Picea abies var. acrocona Transcriptome Shotgun Assembly project

description: Picea abies var. acrocona needle de novo assembly based on Illumina 100 nt paired end reads.
DOI: 10.26036/cnphis0002057
title: Salmonella enterica subsp. enterica serovar Hvittingfoss str. SA20014981 Genome sequencing and assembly

description: Genome sequence of Salmonella Hvittingfoss (serogroup I; 16:b:e,n,x)
DOI: 10.26036/cnphis0002058
title: Salmonella enterica subsp. enterica serovar Itami str. SA20014991 Genome sequencing and assembly

description: Genome sequence of Salmonella Itami (serogroup D; 9,12,:l,z13:1,5)
DOI: 10.26036/cnphis0002059
title: Salmonella enterica subsp. enterica serovar Kentucky str. SA20030505 Genome sequencing and assembly

description: Genome sequence of Salmonella Kentucky (serogroup C2; 8,20:i:z6)
DOI: 10.26036/cnphis0002060
title: Salmonella enterica subsp. enterica serovar Manhattan str. SA20034532 Genome sequencing and assembly

description: Genome sequence of Salmonella Manhattan (serogroup C2; 6,8:d:1,5)
DOI: 10.26036/cnphis0002061
title: Salmonella enterica subsp. enterica serovar Milwaukee str. SA19950795 Genome sequencing and assembly

description: Genome sequence of Salmonella Milwaukee (serogroup U; 43:f,g,[t]:-)
DOI: 10.26036/cnphis0000674
title: Whole genome sequencing of Swedish Salmonella Dublin isolates from cattle

description: Illumina MiSeq genome sequencing of Salmonella Dublin isolates from Swedish cattle, comparing isolates from different regions and outbreaks.
DOI: 10.26036/cnphis0000675
title: Durable coexistence of donor and recipient strains after fecal microbiota transplantation

description: Ten individuals with metabolic syndrome underwent a single faecal microbiota transplantation (FMT): 5 of which were allogenic, the other 5 autologous. Stool samples were collected before FMT (day 0) and days 2, 14, 42 and 84 after FMT; and from the donor before FMT. Metagenomic shotgun sequencing was performed on all samples.
DOI: 10.26036/cnphis0000676
title: Follow_up_studies_in_Africa_of_both_Typhoidal_and_non_typhoidal_Salmonella_infections

description: The rise of Non-Typhoidal Salmonella infections (NTS) continues to cause health problems in many African countries. It is important that the continuing isolation of NTS infections is carefully monitored to identify any new trends or properties as well as changes in the clinical manifestations and any co-localisation with other pathogens. We also aim to follow the continuing isolation of Typhoidal outbreaks that are also being recovered so follow plasmids and resistance profiles along with other potential changes in the genome content. These present studies focus on samples obtained from Uganda, Kenya, Burkina Faso and Ghana. The study plans to examine, via illumine, 230 samples obtained from hospitals in these countries, usually from blood cultures.