cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0001891
title: Balaena mysticetus Genome sequencing

description: The bowhead whale (Balaena mysticetus) has not only been estimated to live over 200 years, making it the longest-lived mammal, but these animals remain disease-free until much more advanced ages than humans can. The mechanisms for the longevity and resistance to aging-related diseases of bowhead whales are unknown, but it is clear they must possess aging prevention mechanisms. In particular in the context of cancer, bowhead whales must have anti-tumour mechanisms, because given their large size and longevity, their cells must have a massively lower chance of developing into cancer when compared to human cells. As such, we sequenced and analysed the genome of the bowhead whale to identify longevity assurance mechanisms. We generated a high-coverage genome assembly of the bowhead whale, which we make available to the scientific community to encourage research using data from long-lived species. Analyses of the genome were also performed to identify promising candidate genes and mechanisms that may explain the long lifespan and resistance to age-related diseases of bowhead whales. Overall, this project provides a key resource for studying the bowhead whale and its exceptional longevity and resistance to diseases. By identifying novel maintenance and repair mechanisms we will learn what is the secret for living longer, healthier lives and may be able apply this knowledge to improve human health and preserve human life.
DOI: 10.26036/cnphis0001892
title: Comparative genomics of 194 Salmonella enterica

description: This genome sequencing project is a collaboration among lab groups at the University of California-Irvine (UCI), The Genome Institute at Washington University in St. Louis and the Bacterial Epidemiology and Antimicrobial Resistance Research Unit (BEAR-RU) at the United States Department of Agriculture. This dataset consists of draft genomes of 194 diverse Salmonella. BEAR-RU analyzed these sequences for genetic variation and genomic context of antibiotic resistance genes. UCI is analyzing these sequences to investigate the evolutionary history of Salmonella.
DOI: 10.26036/cnphis0001893
title: Salmonella enterica subsp. enterica Genome sequencing and assembly

description: Whole genome sequencing of two Salmonella strains isolated from whole broiler chicken carcasses.
DOI: 10.26036/cnphis0001894
title: Dinocras cephalotes Genome sequencing

description: One individual of Dinocras cephalotes was 454 sequenced to generate microsatellite markers and assemble the mitochondrial genome.
DOI: 10.26036/cnphis0001896
title: Drill reference genome project

description: A high quality draft sequence of the reference genome will be assembled from a single sample of Mandrillus leucophaeus, using read data produced by the Illumina platform.
DOI: 10.26036/cnphis0001897
title: Piezodorus guildinii isolate:RBSB-Aug2013 Genome sequencing and assembly

description: The invasive redbanded stink bug, Piezodorus guildinii (Hemiptera: Pentatomidae), has become the dominant stink bug species in the MidSouth of the United States . The goal of this sequencing project is to provide the genomic resource to allow screening for genetic markers for population genetic studies of range expansion of this invasive pest, as well as gene expression studies related to range expansion, host use, and resistance management.
DOI: 10.26036/cnphis0000500
title: Charadrius vociferus Genome sequencing and assembly

description: The whole genome sequencing of Charadrius vociferus
DOI: 10.26036/cnphis0000501
title: Corvus brachyrhynchos Genome sequencing and assembly

description: The whole genome sequencing of Corvus brachyrhynchos
DOI: 10.26036/cnphis0000502
title: Cuculus canorus Genome sequencing and assembly

description: The whole genome sequencing of Cuculus canorus
DOI: 10.26036/cnphis0000503
title: Nannospalax galili Genome sequencing and assembly

description: The whole genome sequencing of Spalax galili
DOI: 10.26036/cnphis0000504
title: Manacus vitellinus Genome sequencing and assembly

description: The whole genome sequencing of Manacus vitellinus
DOI: 10.26036/cnphis0000505
title: Opisthocomus hoazin Genome sequencing and assembly

description: The whole genome sequencing of Opisthocomus hoazin
DOI: 10.26036/cnphis0000506
title: Sus scrofa Genome resequencing

description: Jiangxi Agricultural University pig resequencing project, raw data, 69 pigs
DOI: 10.26036/cnphis0000507
title: Picoides pubescens Genome sequencing and assembly

description: The whole genome sequencing of Picoides pubescens
DOI: 10.26036/cnphis0000509
title: Tinamus guttatus Genome sequencing and assembly

description: The whole genome sequencing of Tinamus guttatus
DOI: 10.26036/cnphis0000510
title: Acanthisitta chloris Genome sequencing and assembly

description: The whole genome sequencing of Acanthisitta chloris
DOI: 10.26036/cnphis0001213
title: Analysis of Unannotated Equine Transcripts Identified by mRNA Sequencing

description: Sequencing of equine mRNA (RNA-seq) identified 428 putative transcripts which do not map to any previously annotated or predicted horse genes. Most of these encode the equine homologs of known protein-coding genes described in other species, yet the potential exists to identify novel and perhaps equine-specific gene structures. A set of 36 transcripts were prioritized for further study by filtering for levels of expression (depth of RNA-seq read coverage), distance from annotated features in the equine genome, the number of putative exons, and patterns of gene expression between tissues. From these, four were selected for further investigation based on predicted open reading frames of greater than or equal to 50 amino acids and lack of detectable homology to known genes across species. Sanger sequencing of RT-PCR amplicons from additional equine samples confirmed expression and structural annotation of each transcript. Functional predictions were made by conserved domain searches. A single transcript, expressed in the cerebellum, contains a putative kruppel-associated box (KRAB) domain, suggesting a potential function associated with zinc finger proteins and transcriptional regulation. Overall levels of conserved synteny and sequence conservation across a 1MB region surrounding each transcript were approximately 73% compared to the human, canine, and bovine genomes; however, the four loci display some areas of low conservation and sequence inversion in regions that immediately flank these previously unannotated equine transcripts. Taken together, the evidence suggests that these four transcripts are likely to be equine-specific. Overall design: Examination of 8 equine RNA samples representing 6 distinct tissues
DOI: 10.26036/cnphis0001214
title: Interaction transcriptome of host wheat and hemibiotrophic fungal pathogen Septoria tritici during disease transition Transcriptome or Gene expression

description: Molecular mechanisms underlying the interplay between fungal pathogenicity and host responses at specific growth phases and the factors triggering disease transition.
DOI: 10.26036/cnphis0001215
title: Genome analysis of Corvus cornix and Corvus corone, hooded and carrion crows

description: Annotated genome of a Hooded Crow (Corvus cornix cornix) individual sampled in Uppsala, Sweden. Genome assembly of a hooded crow (Corvus cornix) individual and whole genome re-sequencing of carrion crow (Corvus corone) and hooded crow (Corvus cornix) population samples. Illumina sequencing data
DOI: 10.26036/cnphis0001216
title: The sequence of Opsanus beta (Gulf Toadfish)

description: Opsanus beta limit chemosensory information given to predators through a unique ‘waste’ nitrogen excretory pattern, in which urea is used to mask the scent of toadfish to predators. This ‘ureotelic strategy’ in turn makes Opsanus beta extremely resistant to ammonia challenge and thus an important model for the suite of human diseases known as hepatic encephalopathy. Hepatic encephalopathy is caused by hepatic failure resulting from chronic alcoholism, acute acetominophen toxicity, and inborn errors of the urea cycle, among other causes.
DOI: 10.26036/cnphis0001217
title: Major food bacterial pathogens in the united states and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, and Vibrio parahaemolyticus genome sequencing

description: University of California at Davis 100K Pathogen Genome Project. Major food bacterial pathogens in the United States and around the world, including Salmonella enterica, E. coli, Shigella, Listeria monocytogenes, Campylobacter Jejuni, Vibrio parahaemolyticus.
DOI: 10.26036/cnphis0001218
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001219
title: Engraulis encrasicolus Genome sequencing

description: Whole genome sequencing in 2 lanes of HiSeq2000 (2x100bp paired-end) of muscle DNA from ten barcoded individuals. Standard post-processing was applied (adaptor clipping and quality checking) and sequences were de-multiplexed.
DOI: 10.26036/cnphis0001221
title: Equus Genome sequencing and assembly

description: In this study, we present a 1.12X draft genome from a horse bone recovered from permafrost dated to ca. 560-780 thousand years before present (Ky BP). For comparison, we sequenced the genome of a Late Pleistocene horse (43 Ky BP), and modern genomes of five domestic horse breeds (E. ferus caballus), a Przewalski horse (E. f. przewalskii), and a donkey (E. asinus).
DOI: 10.26036/cnphis0001222
title: Ladona fulva Genome sequencing and assembly

description: Whole genome sequencing of Ladona fulva using multiple sequencing technologies.
DOI: 10.26036/cnphis0001898
title: Owl monkey reference genome and diversity panel

description: A high quality draft assembly of the genome of Aotus nancymaae will be produced using DNA from a single individual, and read data generated using the Illumina platform. In addition to the deep genome sequence coverage of the reference animal, BCM-HGSC generate whole genome sequences from additional owl monkey individuals in order to identify DNA sequence variation for this species.
DOI: 10.26036/cnphis0001899
title: Anopheles coluzzii whole-genome sequence, and multiplexed shotgun genotyping reads of An. coluzzii, An. merus, and backcross progeny

description: These sequence reads were generated for QTL mapping of backcross progeny of An. merus and An. coluzzii. We created multiplexed shotgun genotyping reads (genome digested with the Mse enzyme) of the backcross progeny, and of the parental species. We also created a standard genomic library (not Mse digested) of An. coluzzii.
DOI: 10.26036/cnphis0001900
title: GenomeTrakr Project: USDA - Food Safety and Inspection Service

description: Whole genome sequencing of cultured STECs as part of the GenomeTrakr surveillance project for rapid source tracking of foodborne illness outbreaks.
DOI: 10.26036/cnphis0001901
title: Apostichopus parvimensis Variation

description: Whole genome assembly and analysis of Parastichopus parvimensis using multiple sequencing technologies.
DOI: 10.26036/cnphis0001902
title: Camelus dromedarius breed:African Genome sequencing and assembly

description: This project aims to sequence and assemble a genome for a domestic dromedary of African origin. The data will provide genetic resources useful for studies of the agricultural and evolutionary importance of camels.
DOI: 10.26036/cnphis0001903
title: RNA-sequencing of healthy human skeletal myocytes

description: Skeletal myocytes are metabolically active and susceptible to insulin resistance, thus implicated in type 2 diabetes (T2D). This complex disease involves systemic metabolic changes and their elucidation at the systems level requires genome-wide data and biological networks. Genome-scale metabolic models (GEMs) provide a network-context to integrate high-throughput data. We generated myocyte-specific RNA-seq data and investigated their correlation with proteome data. These data were then used to reconstruct a comprehensive myocyte GEM. Next, we performed a meta-analysis of six studies comparing muscle transcription in T2D versus healthy subjects. Transcriptional changes were mapped on the myocyte GEM, revealing extensive transcriptional regulation in T2D, particularly around pyruvate oxidation, branched-chain amino acid catabolism, and tetrahydrofolate metabolism, connected through the down-regulated dihydrolipoamide dehydrogenase. Strikingly, the gene signature underlying this metabolic regulation successfully classifies the disease state of individual samples, suggesting that regulation of these pathways is a ubiquitous feature of myocytes in response to T2D. Overall design: Isolated skeletal muscle precursor cells from six normal glucose tolerant and non-obese males and females were differentiated in vitro. RNA from fully differentiated myotubes was sequenced using RNA-seq.
DOI: 10.26036/cnphis0001904
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001905
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0000511
title: Apaloderma vittatum Genome sequencing and assembly

description: The whole genome sequencing of Apaloderma vittatum
DOI: 10.26036/cnphis0000513
title: Buceros rhinoceros silvestris Genome sequencing and assembly

description: The whole genome sequencing of Buceros rhinoceros silvestris.
DOI: 10.26036/cnphis0000514
title: Alligator sinensis Genome sequencing and assembly

description: We chose the Chinese alligator for genome sequencing to reveal molecular evidence of its diving, sensory, and immune adaptations, to provide novel insights into sex chromosome evolution due to its temperature-dependent sex determination, and to help design scientific captive-breeding programs for population recovery project of this endangered species.
DOI: 10.26036/cnphis0000515
title: Antrostomus carolinensis Genome sequencing and assembly

description: The whole genome sequencing of Antrostomus carolinensis
DOI: 10.26036/cnphis0000516
title: Cariama cristata Genome sequencing and assembly

description: The whole genome sequencing of Cariama cristata
DOI: 10.26036/cnphis0000517
title: Cathartes aura Genome sequencing and assembly

description: The whole genome sequencing of Cathartes aura
DOI: 10.26036/cnphis0000518
title: Chlamydotis macqueenii Genome sequencing and assembly

description: The whole genome sequencing of Chlamydotis macqueenii
DOI: 10.26036/cnphis0000519
title: Colius striatus Genome sequencing and assembly

description: The whole genome sequencing of Colius striatus
DOI: 10.26036/cnphis0001224
title: Aedes aegypti strain:Liverpool Genome sequencing

description: Illumina sequencing of separate male and female A. aegypti.
DOI: 10.26036/cnphis0001225
title: Colocasia esculenta Transcriptome or Gene expression

description: The large number of genetic markers using transcriptome sequencing will contribute to research into genetic diversity, marker-assisted selection and trait mapping in Colocasia esculenta.
DOI: 10.26036/cnphis0001226
title: Differential LINE-1 retrotransposition in induced pluripotent stem cells between humans and great apes

description: Understanding cellular and molecular differences between human and non-human primates (NHPs) is essential to the basic comprehension of the evolution and diversity of our own species. Until now, preserved tissues have been the main source of most comparative studies between humans, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). However, these tissue samples do not fairly represent the distinctive traits of live cell behavior, are not amenable to genetic manipulation and do not allow translation of observed differences into phenotypical divergence. We hypothesized that induced pluripotent stem cells (iPSCs) could provide a unique biological resource to elucidate relevant phenotypical differences between human and the great apes and that those differences could have potential adaptation and speciation value. Here, we describe the generation and initial characterization of iPSCs from chimpanzees and bonobos as novel tools to explore our most recent evolution. Comparative gene expression analysis of human and NHP iPSCs revealed differences in regulation of Long Interspersed Nuclear Element (LINE-1 or L1) transposons. A force of change in mammalian evolution, L1 elements are retrotransposons that have remained active during primate evolution. We observed decreased levels of L1 restricting factors APOBEC3B (A3B)7 and PIWIL28 in NHP iPSCs which was correlated with increased human and chimpanzee L1 mobility and endogenous L1 mRNA levels. Moreover, results from manipulation of A3B and PIWIL2 levels in iPSCs suggested a causal inverse relationship between levels of these proteins and L1 activity. Finally, we found increased copy numbers of species-specific L1 elements in the genome of chimpanzees compared to humans, supporting the idea that increased L1 mobility in NHPs is not limited to iPSCs in culture and may have also occurred in the germline during primate evolution. We propose that differences in L1 mobility may have differentially shaped the genomes of humans and NHPs and could have had an adaptive significance. Overall design: polyA RNA-Seq profiling of iPS cells from human, chimpanzee, and bonobo, and small RNA-Seq profiling of human iPS cells.
DOI: 10.26036/cnphis0001227
title: Diabrotica virgifera virgifera non-diapauising (ND) strain

description: Illumina HiSeq reads obtained from sequencing total genomic libraries generated from a pooled collection of 50 adult beetles from the non-diapausing strain of the Western corn rootworm.
DOI: 10.26036/cnphis0001228
title: Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

description: We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol with 500–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. We discovered classes of DNA-binding factors that strictly avoided, could tolerate or tended to overlap with the nucleosome. Using ATAC-seq maps of human CD4+ T cells from a proband obtained on consecutive days, we demonstrated the feasibility of analyzing an individual’s epigenome on a timescale compatible with clinical decision-making. Overall design: We examined chromatin structure using ATAC-seq in 2 cell types (GM12878 cell line, purified CD4+ T cells).
DOI: 10.26036/cnphis0001229
title: Pyrus x bretschneideri strain:Dangshansuli Transcriptome or Gene expression

description: Do novo sequencing Pyrus bretshneideri Rehd. cv. Dangshansuli peel fruit.
DOI: 10.26036/cnphis0001230
title: Elseya albagula Genome sequencing

description: Low-coverage shotgun sequencing was used to randomly sample genomic sequence data for microsatellite repeats in the Australian snapping turtle, Elseya albagula, in order to develop a suite of polymorphic microsatellite markers for use in population genetic and paternity studies.
DOI: 10.26036/cnphis0001231
title: Aspergillus glaucus CBS 516.65 Genome sequencing and assembly

description: Comparative analysis of Aspergilli to facilitate novel strategies in fungal biotechnology
DOI: 10.26036/cnphis0001233
title: A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequence Quality Control consortium

description: We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the United States Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for sequence discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with &gt;80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed, for these and qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcriptlevel profiling. The complete SEQC data sets, comprising &gt;100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings. Overall design: The well-characterized reference RNA samples A (pooled cell lines) and B (human brain) from the MAQC consortium, adding spike-ins of synthetic RNA from the External RNA Control Consortium (ERCC). Samples C and D were then constructed by combining A and B in known mixing ratios, 3:1 and 1:3, respectively. All samples were distributed to several independent sites for RNA-Seq library construction and profiling by Illumina HiSeq 2000 and LifeTech SOLiD 5500 platforms. Also, vendors created their own cDNA libraries that were then distributed to each test site, in order to examine the degree of a ?site effect? that was independent of the library preparation process. To support an assessment of gene models, samples A and B were also sequenced at independent sites by the Roche 454 platform, providing longer reads. For comparison to other technologies, these data were also compared to the MAQC-I Affymetrix U133 Plus2 microarray, several current microarray platforms, and also assessed by 20,801 PrimePCR reactions. Sample A: Universal Human Reference RNA (UHRR) from Stratagene and ERCC Spike-In controls Sample B: Human Brain Reference RNA (HBRR) from Ambion and ERCC Spike-In controls Sample C: Mix of A and B (3:1) Sample D: Mix of A and B (1:3) Sample E: Ambion ERCC Spike-In Control Mix 1 Sample F: Ambion ERCC Spike-In Control Mix 2
DOI: 10.26036/cnphis0001906
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001907
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001908
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001909
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001910
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001911
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001912
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001913
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001914
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001915
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0000520
title: Spermophilus dauricus WGS project

description: Spermophilus dauricus is the well characterized ground squirrel in northeast Asia, which belongs to the same genus as those live in North America, e.g., Spermophilus tridecemlineatus. Recent studies showed that during the adaptive interaction with hibernation, Spermophilus dauricus inherited unique functional feathers that are of medical significance, such as its resistance to hypothermia, arrhythmia and hypoxia. The genome sequencing of Spermophilus dauricus may not only explains the interesting zoological phenomenon of hibernation, but also provides an essential basis for exploring the possibility to apply hibernation strategies in clinical medicine.
DOI: 10.26036/cnphis0000521
title: Eurypyga helias Genome sequencing and assembly

description: The whole genome sequencing of Eurypyga helias