cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000522
title: Fulmarus glacialis Genome sequencing and assembly

description: The whole genome sequencing of Fulmarus glacialis
DOI: 10.26036/cnphis0000523
title: Gavia stellata Genome sequencing and assembly

description: The whole genome sequencing of Gavia stellata
DOI: 10.26036/cnphis0000524
title: Haliaeetus albicilla Genome sequencing and assembly

description: The whole genome sequencing of Haliaeetus albicilla
DOI: 10.26036/cnphis0000525
title: Leptosomus discolor Genome sequencing and assembly

description: The whole genome sequencing of Leptosomus discolor
DOI: 10.26036/cnphis0000526
title: Merops nubicus Genome sequencing and assembly

description: The whole genome sequencing of Merops nubicus
DOI: 10.26036/cnphis0000527
title: Mesitornis unicolor Genome sequencing and assembly

description: The whole genome sequencing of Mesitornis unicolor
DOI: 10.26036/cnphis0000529
title: Pelecanus crispus Genome sequencing and assembly

description: The whole genome sequencing of Pelecanus crispus
DOI: 10.26036/cnphis0001234
title: Emydura macquarii krefftii Genome sequencing

description: Low-coverage shotgun sequencing was used to randomly sample genomic sequence data for microsatellite repeats in Krefft''s river turtle, Emydura macquarii krefftii, from Australia, in order to develop a suite of polymorphic microsatellite markers for use in population genetic analyses.
DOI: 10.26036/cnphis0001235
title: Bactrocera dorsalis strain:Punador Genome sequencing and assembly

description: Whole genome shotgun DNA sequencing and assembly was performed on a laboratory colony of B. dorsalis.
DOI: 10.26036/cnphis0001236
title: RNA-seq of RNase R treated poly(A)-/ribo- RNAs from H9 cells

description: We have used RNA-seq to examine circular RNAs from RNase R treated poly(A)-/ribo- RNAs in human embryonic stem cells Overall design: Examine circular RNAs in human embryonic stem cells
DOI: 10.26036/cnphis0001237
title: Anas platyrhynchos strain:Shaoxing Transcriptome or Gene expression

description: All-rebundant sequences of duck liver by RNA-seq and de novo assembly.
DOI: 10.26036/cnphis0001238
title: Foodborne Pathogen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001239
title: Evaluation of targeted enrichment of Mammuthus mitogenomes

description: Raw Illumina read files associated with Enk et al. publication on qPCR as a predictor of mapped reads after enrichment. Sequence data from non-enriched and enriched libraries deriving from Pleistocene-age bone and tooth remains of various Mammuthus sp.
DOI: 10.26036/cnphis0001240
title: Chickspress

description: Lack of genome structural- and functional-annotation significantly prevents researchers from exploiting the full potential of the chicken genome model system for comparative and functional genomic studies. Our objective is to make the chicken genome annotation much more comprehensive and useful for comparative and functional genomic studies by integrating experimental annotation with standardized gene symbols and functional annotation to make all of this information easily accessible to the biomedical research community. Transcriptomic (mRNA- and small-RNAseq), proteomic and proteogenomic mapping data were combined for the purpose of experimental annotation.
DOI: 10.26036/cnphis0001241
title: Cyprinus carpio ''Songpu mirror carp'' Genome sequencing

description: Common carp (Cyprinus carpio) is one of the most important aquaculture species in the world and has a diversity of phenotypes on skin coloration, color patterning, scalation, body shape and fin shape. Moreover, common carp genome may be involved an additional round of whole genome duplication (WGD) than most other teleost fishes. Sequencing of the common carp genome aims to characterize and understand its genomic and genetic feature. The sequenced individual was a gynogenetic Song pu mirror carp produced by heat shock treatment.
DOI: 10.26036/cnphis0001242
title: Tachyglossus aculeatus strain:unknown Genome sequencing

description: Genome sequencing data for two echidna (T. aculeatus) individuals, one male and one female.
DOI: 10.26036/cnphis0001916
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001917
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001918
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001919
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001920
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001921
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001922
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001923
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001924
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0000528
title: Nestor notabilis Genome sequencing and assembly

description: The whole genome sequencing of Nestor notabilis
DOI: 10.26036/cnphis0000530
title: Phaethon lepturus Genome sequencing and assembly

description: The whole genome sequencing of Phaethon lepturus
DOI: 10.26036/cnphis0000531
title: Phalacrocorax carbo Genome sequencing and assembly

description: The whole genome sequencing of Phalacrocorax carbo
DOI: 10.26036/cnphis0000532
title: Phoenicopterus ruber ruber Genome sequencing and assembly

description: The whole genome sequencing of Phoenicopterus ruber ruber
DOI: 10.26036/cnphis0000533
title: Podiceps cristatus Genome sequencing and assembly

description: The whole genome sequencing of Podiceps cristatus
DOI: 10.26036/cnphis0000534
title: Pterocles gutturalis Genome sequencing and assembly

description: The whole genome sequencing of Pterocles gutturalis
DOI: 10.26036/cnphis0000535
title: Tauraco erythrolophus Genome sequencing and assembly

description: The whole genome sequencing of Tauraco erythrolophus
DOI: 10.26036/cnphis0000536
title: Tyto alba Genome sequencing and assembly

description: The whole genome sequencing of Tyto alba
DOI: 10.26036/cnphis0000537
title: Fukomys damarensis Genome sequencing and assembly

description: Whole genome sequence of A 5-year old male Fukomys damarensis.
DOI: 10.26036/cnphis0001243
title: Megaderma lyra Genome sequencing and assembly

description: Megaderma lyra (greater false vampire bat) genome sequencing
DOI: 10.26036/cnphis0001244
title: Pteronotus parnellii Genome sequencing and assembly

description: Pteronotus parnellii (Parnell''s mustached bat) genome sequencing
DOI: 10.26036/cnphis0001245
title: Rhinolophus ferrumequinum Genome sequencing and assembly

description: Rhinolophus ferrumequinum (greater horseshoe bat) genome sequencing
DOI: 10.26036/cnphis0001246
title: Salmonella enterica subsp. enterica serovar 4,[5],12:i:- str. 08-1736 genome sequencing project.

description: Salmonella is an important foodborne pathogen.
DOI: 10.26036/cnphis0001247
title: Genomic reads for 3 snakes: Boa constrictor, Thamnophis elegans and Sistrurus miliarius. Genome sequencing

description: Genomic sequencing of boa (Boa constrictor), garter snake (Thamnophis elegans) and pygmy rattlesnake (Sistrurus miliarius).
DOI: 10.26036/cnphis0001248
title: Salmonella enterica subsp. enterica serovar Typhimurium str. STm1 Genome sequencing

description: A variant of S. Typhimurium phage type 135, STm135@, is one of the most common forms of S. Typhimurium responsible for foodborne gastroenteritis in Australia and has been associated with multiple outbreaks. To facilitate studies of STm135@ and future outbreak investigations relating to this pathogen, the genomes of 12 STm135@ isolates linked to egg-associated outbreaks in Tasmania were sequenced.
DOI: 10.26036/cnphis0001249
title: Ephestia kuehniella strain:strain L Genome sequencing

description: Evoution of the W chromosome.
DOI: 10.26036/cnphis0001250
title: Salmonella enterica subsp. enterica serovar Typhimurium str. STm9 Genome sequencing

description: A variant of S. Typhimurium phage type 135, STm135@, is one of the most common forms of S. Typhimurium responsible for foodborne gastroenteritis in Australia and has been associated with multiple outbreaks. To facilitate studies of STm135@ and future outbreak investigations relating to this pathogen, the genomes of 12 STm135@ isolates linked to egg-associated outbreaks in Tasmania were sequenced.
DOI: 10.26036/cnphis0001251
title: Salmonella enterica subsp. enterica serovar Typhimurium str. STm10 Genome sequencing

description: A variant of S. Typhimurium phage type 135, STm135@, is one of the most common forms of S. Typhimurium responsible for foodborne gastroenteritis in Australia and has been associated with multiple outbreaks. To facilitate studies of STm135@ and future outbreak investigations relating to this pathogen, the genomes of 12 STm135@ isolates linked to egg-associated outbreaks in Tasmania were sequenced.
DOI: 10.26036/cnphis0001925
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001926
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001927
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001928
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001929
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001930
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001931
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001932
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001933
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0000538
title: High-depth whole genome sequencing of 760 vascular plants with specimens and images available Raw sequence reads

description: a large dataset of vascular plants, with both the high-depth whole genome sequencing data and the voucher specimen, making it valuable dataset for plant genome researches and applications.
DOI: 10.26036/cnphis0000551
title: Phylogeography of Salmonella Typhimurium

description: A highly invasive form of non-typhoidal Salmonella (iNTS) disease has recently been documented in many countries in sub-Saharan Africa. The most common Salmonella enterica serovar causing this disease is Typhimurium (Salmonella Typhimurium). We applied whole-genome sequence-based phylogenetic methods to define the population structure of sub-Saharan African invasive Salmonella Typhimurium isolates and compared these to global Salmonella Typhimurium populations. Notably, the vast majority of sub-Saharan invasive Salmonella Typhimurium isolates fell within two closely related, highly clustered phylogenetic lineages that we estimate emerged independently ?52 and ?35 years ago in close temporal association with the current HIV pandemic. Clonal replacement of isolates from lineage I by those from lineage II was potentially influenced by the use of chloramphenicol for the treatment of iNTS disease. Our analysis suggests that iNTS disease is in part an epidemic in sub-Saharan Africa caused by highly related Salmonella Typhimurium lineages that may have occupied new niches associated with a compromised human population and antibiotic treatment. 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/cnphis0000552
title: A draft sequence and preliminary analysis of the Neandertal genome

description: A draft sequence of the Neandertal genome composed of over 3 billion nucleotides from three individuals. Through comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world allowed the analysis of admixture between Neandertals and ancestral modern humans, as well as the identifcation of a number of genomic regions that may have been affected by positive selection in ancestral modern humans.
DOI: 10.26036/cnphis0000553
title: Study of Salmonella enterica diversity

description: For further information on this study please see http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000554
title: MDR invasive NTS S. Typhimurium strains

description: For further information on this study please see http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000555
title: Salmonella nitra genome sequencing

description: For further information on this study please see http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000556
title: Salmonella dublin & pullorum

description: For further information on this study please see http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000557
title: Monophasic Salmonella isolates

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/cnphis0001252
title: Salmonella enterica subsp. enterica serovar Typhimurium str. STm11 Genome sequencing

description: A variant of S. Typhimurium phage type 135, STm135@, is one of the most common forms of S. Typhimurium responsible for foodborne gastroenteritis in Australia and has been associated with multiple outbreaks. To facilitate studies of STm135@ and future outbreak investigations relating to this pathogen, the genomes of 12 STm135@ isolates linked to egg-associated outbreaks in Tasmania were sequenced.
DOI: 10.26036/cnphis0001253
title: Salmonella enterica subsp. enterica serovar Typhimurium str. STm12 Genome sequencing

description: A variant of S. Typhimurium phage type 135, STm135@, is one of the most common forms of S. Typhimurium responsible for foodborne gastroenteritis in Australia and has been associated with multiple outbreaks. To facilitate studies of STm135@ and future outbreak investigations relating to this pathogen, the genomes of 12 STm135@ isolates linked to egg-associated outbreaks in Tasmania were sequenced.
DOI: 10.26036/cnphis0001254
title: Salmonella enterica subsp. enterica serovar Typhimurium str. STm5 Genome sequencing

description: A variant of S. Typhimurium phage type 135, STm135@, is one of the most common forms of S. Typhimurium responsible for foodborne gastroenteritis in Australia and has been associated with multiple outbreaks. To facilitate studies of STm135@ and future outbreak investigations relating to this pathogen, the genomes of 12 STm135@ isolates linked to egg-associated outbreaks in Tasmania were sequenced.
DOI: 10.26036/cnphis0001255
title: Single Human Oocyte Genome sequencing

description: Single cell genomic analyses are critical for reproductive biology since each germline cell has a unique genome due to homologous recombination. Genomes of single sperm cells have been sequenced recently. Similar genomic analyses on oocytes are highly desirable because their importance for not only meiosis research, but also in vitro fertilization (IVF), i.e. selecting oocytes free of aneuploidy and point mutations associated with Mendelian diseases. Here we performed whole genomic amplification and sequencing of human oocytes using multiple annealing and looping based amplification cycle (MALBAC).
DOI: 10.26036/cnphis0001256
title: Pygoscelis adeliae Genome sequencing

description: Genomic sequencing data for modern and ancient Adelie penguin (Pygoscelis adeliae).
DOI: 10.26036/cnphis0001257
title: Linum usitatissimum strain:Cultivar Transcriptome or Gene expression

description: Flax is grown for its use as an edible oil, as a nutritional supplement. it''s fibers are used to make linen. Flax seeds contain high levels of dietary fiber as well as lignans, an abundance of micronutrients and omega-3 fatty acids.
DOI: 10.26036/cnphis0001258
title: Baboon genome sequencing project and diversity panel

description: The Baylor College of Medicine Human Genome Sequencing Center is sequencing and assembling the genome of the baboon (genus Papio). A high quality draft sequence of the reference genome has been produced from an olive baboon (Papio anubis), using read data produced by the Sanger, 454 and Illumina platforms. The latest version of the baboon genome adds Pacific Biosciences RS long reads (12x whole genome coverage) using DNA from an animal that comes from the same population as of the reference animal. The RS reads were mapped and gaps filled in the existing assembly using PBJelly2 software (English, Richards et al. 2012). In addition to the deep sequence coverage of the reference olive baboon, BCM-HGSC has generated whole genome coverage from additional olive baboons, as well as individuals representing hamadryas (P. hamadryas), Guinea (P. papio), yellow (P. cynocephalus), chacma (P. ursinus) kinda (P. kindae) baboons and Gelada (Theropithecus gelada), an outgroup to Papio. Comparative analyses of these data are in progress and will result in a description of genomic diversity within and among species of the genus Papio and it’s close relatives. Baboons are important both as a well-studied and diverse evolutionary radiation of Old World monkeys, and as laboratory primates commonly used in biomedical research. Although closely related, the species within this genus differ in social behavior, ecology, body size and other fundamental characteristics. In the laboratory, baboons are used as models of several human diseases, including cardiovascular disease, obesity, hypertension, epilepsy, infectious disease and various aspects of basic neurobiology. The project is funded by the National Human Genome Research Institute (NHGRI).
DOI: 10.26036/cnphis0001259
title: Caenorhabditis elegans, Caenorhabditis briggsae MA line Genome sequencing

description: Variation in base-substitution mutation in experimental and natural lineages of Caenorhabditis nematodes
DOI: 10.26036/cnphis0001260
title: Genetic variation within the North American Sage-grouse genus Centrocercus (class Aves)

description: Evaluation of genetic differentiation within the Sage-grouse genus Centrocercus. Three geographically distinct samples of North American Sage-grouse, genus Centrocercus (class Aves). Two samples are taxonomically considered Greater Sage-grouse (Centrocercus urophasianus) and the third is considered Gunnison Sage-grouse (Centrocercus minimus). Ten individual monoisolates were obtained for each group.
DOI: 10.26036/cnphis0001934
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001935
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001936
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001937
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001938
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001939
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001940
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001941
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001942
title: Foodborne Pathogen Survey

description: Genome Sequencing Project.
DOI: 10.26036/cnphis0000558
title: Mali iNTS - Dublin & Enteritidis

description: For further information on this study please see http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html
DOI: 10.26036/cnphis0000559
title: Salmonella Typhimurium DT104 isolates

description: "Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts." Pubmed ID: 24030491. The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, with an unprecedented national collection of isolates collected contemporaneously from humans and animals and including a sample of internationally derived isolates, we have used whole-genome sequencing to dissect the phylogenetic associations of the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, which emphasizes the critical importance of integrated genotypic data sets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.
DOI: 10.26036/cnphis0000560
title: Distinct patterns of somatic alterations between normal and tumor genomes

description: The main objective of this project is to develop a sequencing strategy to efficiently define the complete catalog of mutations present in the breast tumor cell line HCC1954. Strategies for targeting gene rich regions of the genome, such as exon capture and construction of reduced representation libraries will be combined with shotgun and paired-end sequencing. Parallel sequencing of a lymphoblastoid cell line (HCC1954BL), derived from the same breast cancer patient, will be use to accurately distinguish mutations from polymorphisms.