cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0001330
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001332
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002007
title: The landscape of accessible chromatin in mammalian pre-implantation embryos (ATAC-Seq)

description: In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development. Overall design: Mouse preimplantation embryos were obtained from crosses of C57BL/6N and DBA/2N. ATAC-seq was performed in these embryos at various stages in preimplantation development.
DOI: 10.26036/cnphis0002008
title: Drop-Seq analysis of mixtures of human (HEK) and mouse (3T3) cells (1000/100 STAMPs) at 12.5 cells per microliter

description: A cell supsension containing an equal mix of HEK and 3T3 cells was used in Drop-Seq, a novel technology for high-throughput single cell mRNAseq. Cells were mixed at a final concentration of 12.5 cells per microliter in droplets. Overall design: An estimated 570 STAMPs were selected for amplification.
DOI: 10.26036/cnphis0002009
title: Drosophila miranda Genome sequencing

description: Genomic resequencing of isofemale lines for LD-based inference of recombination rate
DOI: 10.26036/cnphis0002010
title: Sex chromosome evolution in the threespine stickleback

description: Whole-genome sequencing of marine threespine sticklebacks to study X and Y chromosome evolution.
DOI: 10.26036/cnphis0002011
title: A prospective, longitudinal analysis of the developing gut microbiome in infants en route to type 1 diabetes

description: This is a prospective, longitudinal collection of stool samples from infants at risk for disease. Infants from Finland and Estonia were recruited at birth based on HLA risk genotyping. Parents collected their infants’ stool at approximately monthly intervals and promptly stored the sample in the freezer prior to shipment for sample processing and sequencing. The cohort comprised of 33 infants, 11 of which seroconverted to serum autoantibody positivity and of those, four developed T1D within the three year time-frame of this study.
DOI: 10.26036/cnphis0002012
title: Primary duck hepatocyte transcriptome analysis provides insight into the host innate immune response and hepadnavirus infection

description: Our aim was to classify and quantify transcripts identified in 24-h-cultured primary duck hepatocytes and construct a protein–protein interaction network to serve as a reference for host factors associated with hepadnavirus infection. Methods: The transcriptome of 24h-cultured PDHs was analyzed by the pair-end sequencing on the Illumina Solexa platform. High-quality reads were mapped to the Anas platyrhynchos genome with TopHat v2.0.12 software. TopHat allows multiple alignments per read and default parameters were used. Cufflinks v2.2.1 software was later used for analyses that included transcript assembly and FPKM value calculations to quantify gene expression; this program was also run with default parameters. Results: A total of 87.8 million high-quality reads were obtained from three primary duck hepatocyte samples isolated from three separate 1-day-old Anas domesticus ducklings. The reads (mean length 92.21 bases) were mapped to the Anas platyrhynchos genome. A total of 13,541 genes with &gt; 1 fragments per kilobase of transcript per million mapped reads values were expressed in the 24-h-cultured primary duck hepatocyte samples.Using gene ontology analysis, expressed genes were assigned to functional categories. A total of 182 genes expressed in all three separate primary duck hepatocyte samples were identified as liver-specific genes. Conclusions: Transcriptome and gene ontology analyses of 24-h-cultured primary duck hepatocytes indicate that these cells retain hepatocyte-specific biological characteristics and can be used as a model system for hepadnavirus infection. A novel protein–protein interaction network suggests that host factors regulating or inhibiting innate immunity are directly associated with hepadnavirus. Overall design: The transcriptome of 24h-cultured PDHs was analyzed by the paired-end sequencing on the Illumina Solexa platform.
DOI: 10.26036/cnphis0002013
title: Pacific oyster Crassostrea gigas (Bivalvia, Mollusca), Pacific abalone Haliotis discus hannai (Gastropoda, Mollusca), and the sand worm Perinereis aibuhitensis (Polychaeta, Annelida) Raw sequence reads

description: Evolutionary development analysis on the Spiralians
DOI: 10.26036/cnphis0002014
title: Wuchereria bancrofti isolate:PNG22 Variation

description: Our goal was to sequence and assembly the genome of Wuchereria bancrofti in an effort to identify SNPs for future population studies.
DOI: 10.26036/cnphis0002015
title: Cyanopica cyanus Transcriptome or Gene expression

description: To reveal the genetic basis of animal behavioral personality traits of Boldness and Shyness
DOI: 10.26036/cnphis0002016
title: Genomic resource of landsnail, Aegista diversifamilia

description: Genomic resources of Stylommatophora were very rare despite the high biodiversity of landsnails.
DOI: 10.26036/cnphis0000631
title: Th single cell RNA-Seq

description: Th2 cells regulate helminth infections, allergic disorders, tumor immunity and pregnancy by secreting various cytokines. It is likely that there are undiscovered Th2-signaling molecules. While steroids are known to be immunoregulators, de novo steroid production from immune cells has not been previously characterised. We demonstrate production of the steroid pregnenolone by Th2 cells in vitro, and in vivo in a helminth infection model. To identify gene-expression identify of these steroidogenic-Th2 cells, we performed single-cell RNA-sequencing.
DOI: 10.26036/cnphis0000632
title: Sheep Tissue Atlas

description: Sheep total RNA was extracted from embryonic and adult tissues. Sequencing libraries were prepared from the RNA using the Illumina TruSeq stranded total RNA with the Ribo Zero gold option for the rRNA removal. The fragmentation in the standard protocol was modified to increase the average insert size in the library. Sequencing with 151 base paired end reads was performed on an Illumina HiSeq 2500 in rapid mode.
DOI: 10.26036/cnphis0000633
title: Solving the problem of comparing whole bacterial genomes across different sequencing platforms

description: Whole genome sequencing (WGS) shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one technology because each technology has a systematic bias making integration of data generated from different platforms difficult. We developed two different procedures for identifying variable sites and inferring phylogenies in WGS data across multiple platforms. The methods were evaluated on three bacterial data sets sequenced on three different platforms (Illumina, 454, Ion Torrent). We show that the methods are able to overcome the systematic biases caused by the sequencers and infer the expected phylogenies. It is concluded that the cause of the success of these new procedures is due to a validation of all informative sites that are included in the analysis. The procedures are available as web tools.
DOI: 10.26036/cnphis0000634
title: Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Previous studies have shown an association between the gut microbiota and liver complications such as cirrhosis and other liver injuries. We therefore undertook a whole gut microbiome wide association study of stool samples from 98 liver cirrhosis patients and 83 healthy controls to characterise the faecal microbial communities and their functional composition. In total, we generated 860 Gb of high-quality sequence data and built a reference gene set for the liver cirrhosis cohort containing 2.69 million genes, 36.1% of which was not covered by previously published gene catalogues.

description: Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Previous studies have shown an association between the gut microbiota and liver complications such as cirrhosis and other liver injuries. We therefore undertook a whole gut microbiome wide association study of stool samples from 98 liver cirrhosis patients and 83 healthy controls to characterise the faecal microbial communities and their functional composition. In total, we generated 860 Gb of high-quality sequence data and built a reference gene set for the liver cirrhosis cohort containing 2.69 million genes, 36.1% of which was not covered by previously published gene catalogues.
DOI: 10.26036/cnphis0000635
title: Sequencing_Nigerian_Salmonella_Typhi_samples

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000636
title: Isolation of a Salmonella Kentucky ST-198 strain and its H2S-negative variant from the same patient.

description: Hydrogen sulfide production is a characteristic feature in the laboratory identification of Salmonella species. Ciprofloxacin-resistant Salmonella Kentucky ST-198 arose in Egypt and spread worldwide. We isolated a H2S-negative and a H2S- positive variants of the strain from the sacral wound and stool respectively of the same patient in Kuwait. Whole genome sequencing of the isolates showed that the H2S-negative variant differed in having an insertion of a base in the gene encoding molybdenum cofactor biosynthesis protein c leading to a frame-shift mutation. This gene is linked to the thiosulfate reductase gene involved in the production of H2S. This seems to be a novel mechanism in H2S-negative variant generation in salmonella. Lack of production of H2S can potentially lead to failure of detection of salmonella in the laboratory.
DOI: 10.26036/cnphis0000637
title: Investigation_of_temporo_spatial_and_carriage_invasion_relationships_between_isolates_of_Salmonella_Typhimurium_from_a_well_described_paediatric_cohort_in_Malawi

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000638
title: A genomic dissection of travel associated ESBL producing Salmonella Typhi originating from the Philippines - A one-off occurrence or threat to the effective treatment of typhoid?

description: ESBL producing Typhi has only been confirmed in a few cases. We surveyed the global occurrence and identified one new case. This resembled epidemiological a previously published strain why the two were compared by whole genome sequencing. Both isolates were acquired in the Philippines in 2007. They shared the same susceptibility profile, contained the same antimicrobial resistance genes; blaSHV-12, blaTEM-1, aac(6')IIc, strA, strB, tetD, and dfrA18, belonged to MLST ST1, haplotype H13, no chromosomal or plasmid SNP differences, and contained the incHI2/HI2A of 280 kb. Minor differences were observed in pulsotypes and one isolate contained a 144kb deletion of the SPI-7. These isolates likely belong to an undetected outbreak. The question is if this is a one-off occurrence or a threat to the future effective treatment of typhoid fever with severe public health implications – we call for a survey to search for persistence.
DOI: 10.26036/cnphis0000639
title: Gene expression pattern of single mES cells during cell cycle stages

description: In this study, we aimed to study the gene expression patterns at single cell level across the different cell cycle stages in mESC. We performed single cell RNA-Seq experiment on mESC that were stained with Hoechst 33342 and Flow cytometry sorted for G1, S and G2M stages of cell cycle. Single cell RNA-Seq was performed using Fluidigm C1 system and libraries were generated using Nextera XT (Illumina) kit.
DOI: 10.26036/cnphis0001331
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001333
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001334
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001335
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001336
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001337
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001338
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001339
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001340
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001341
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002017
title: song sparrow (Melospiza melodia) 454 sequences from five females

description: Five female song sparrows were sequenced to find microsatellite loci for linkage map construction and measuring heterozygosity.
DOI: 10.26036/cnphis0002018
title: Rapid assembly of taxonomically validated mitochondrial genomes from historical insect collections - Raw sequence reads

description: Illumina shotgun sequencing was used to obtain full and partial mitochondrial genomes from degraded DNA of dry-pinned insect specimens (butterflies).
DOI: 10.26036/cnphis0002019
title: Genomic resource of landsnail, Dolicheulota formosensis

description: Genomic resources of Stylommatophora were very rare despite the high biodiversity of landsnails.
DOI: 10.26036/cnphis0002020
title: Larimichthys crocea Variation

description: The whole genome sequencing for marker development
DOI: 10.26036/cnphis0002021
title: GenomeTrakr Project: Hawaii State Department of Health - HSLD

description: Whole genome sequencing of cultured Salmonella enterica as part of the US Food and Drug Administration''s WGS surveillance effort for the rapid detection of foodborne illness outbreaks.
DOI: 10.26036/cnphis0002022
title: Drosophila Raw sequence reads

description: To determine the role of chromosomal inversions in the speciation process. We compared the genomic divergence between two D. mojavensis and one D. arizonae populations and found an increase in pairwise divergence at rearranged compared to colinear chromosomes. We used the density of divergent sites in short blocks of intergenic sequence, to fit a series of models of isolation with gene flow to populations of D. mojavensis and D. arizonae in allopatry and sympatry. These analyses suggest that i) D. mojavensis and D. arizonae have experienced post-divergence gene flow which however ceased around 270 KY ago ii) gene flow was significantly reduced in chromosomes harbouring fixed inversion differences and iii) that at least some of these inversions originated around the onset of species divergence. Taken together, these results support those recent models of speciation with gene flow which suggest that inversions arising during or after the onset of species divergence can play a crucial role in the build-up of reproductive isolation.
DOI: 10.26036/cnphis0002023
title: Agricultural soil and sugarcane root microbial community Raw sequence reads

description: The study aims to profile the sugarcane root microbiome and investigate the effects of industry standard nitrogen fertiliser application on the microbial community composition of the root microbiome and surrounding bulk soil, using high-throughput 16S rRNA gene amplicon profiling and metagenomics.
DOI: 10.26036/cnphis0002024
title: Soil beetle communities from South Iberia

description: The main aim of the study is showing the high diversity and turnover of soil beetles communities using the high phylogenetic resolution provided by long mitochondrial DNA sequences obtained with free PCR metagenomic approaches.
DOI: 10.26036/cnphis0000640
title: Genomic Signature of Multi-Drug Resistant Salmonella Typhi related to a Massive Outbreak in Zambia during 2010 - 2012.

description: Retrospectively, we investigated the epidemiology of a massive Salmonella enterica serovar Typhi outbreak in Zambia during 2010 to 2012. Ninety-four isolates were susceptibility tested by MIC determinations. Whole genome sequence typing (WGST) of 33 isolates and bioinformatic analysis identified the MLST, haplotype, plasmid replicon, antimicrobial resistance genes, and the genetic relatedness by Single Nucleotide Polymorphism (SNP) analysis and genomic deletions. The outbreak affected 2,040 patients with a fatality rate of 0.5%. Most isolates (83.0%) were multi-drug resistant (MDR). The isolates belonged to MLST ST1 and a new variant of the haplotype; H58B. Most isolates contained a chromosomally translocate region containing seven antimicrobial resistance genes; catA1, blaTEM-1, drfA7, sul1/2, and strA/B, fragments of incQ1plasmid replicon, IP type 2 integron, and the mer operon. The isolates were clonal diversified containing 35 deletions, 415 SNPs and 21 bifurcation points in the phylogenetic tree with relation to strains from India and Central Africa. The phylogenetic analysis and deletion content clearly indicated that the isolates involved in the outbreak were only distantly related suggesting that multiple clones and lineages were responsible for the outbreak. In contradiction to the common view that the emerging global S. Typhi haplotype; H58B, contains the MDR incHI1 plasmid is responsible for the majority of typhoid infections; we found that a new variant of the haplotype harbouring a chromosomally translocated region containing the MDR islands of incHI1 plasmid emerged in Zambia. This will chance the perception of the term “classical MDR” currently being associated with the incHi1 plasmid.
DOI: 10.26036/cnphis0000641
title: A_molecular_epidemiology_study_of_the_occurrence_and_control_of_Salmonella_in_duck_breeding_and_production

description: http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000642
title: Speciation with gene flow in equids despite extensive chromosomal plasticity

description: Horses, asses and zebras belong to a single genus, Equus, which emerged 4.0-4.5 million years ago (mya). Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here, we present 6 genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto only represented by the horse and the domestic donkey. Additionally, we used a museum specimen to characterize the genome of the Quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 thousand years (kyr) following major climatic events. We show that the earliest speciation occurred with gene flow in Northern America and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1-3.4 mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow and, ultimately, speciation.
DOI: 10.26036/cnphis0000643
title: A role for portable single-molecule nanopore sequencing in the management of a hospital Salmonella outbreak

description: Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting over 30 patients in our hospital. This outbreak was linked to community cases as well as cases detected nationally and Europe-wide. The potential risk posed to hospital patients with Salmonella is high and demands rapid action. We investigated, for the first time, the potential of the Oxford Nanopore MinION™, a portable, laptop-driven, real-time single-molecule whole-genome sequencer for the rapid detection of outbreak strains. We integrated data from this platform with a thorough outbreak investigation undertaken prospectively on the Illumina MiSeq platform. This outbreak was placed into national context by integration with whole-genome data from surveillance genome data produced by Public Health England. Our results show the MinION™ can identify the bacterial species and serotype of a sample within 30 minutes, and determine to single nucleotide level if a sample is part of the outbreak within 2 hours. This novel, multi-tiered approach using genome sequencing and integration of digital datasets represents a possible technological paradigm for future outbreaks and may have impact on infection control practices.
DOI: 10.26036/cnphis0000644
title: Salmonella Typhi H58 antibiotic resistance island

description: Here, we report the use of the MinION to resolve the structure of a composite transposon, encoding multidrug resistance, in Salmonella Typhi Haplotype 58 - a multidrug resistant strain that has undergone global expansion. MinION data from a single 18-hour run was used to scaffold Illumina data and identify the chromosomal insertion site and structure of the island.