cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0002375
title: Patagioenas fasciata genome sequencing and assembly

description: Long-range assembly of the genome of the band-tailed pigeon, the closest extant relative of the extinct passenger pigeon
DOI: 10.26036/cnphis0002376
title: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes in Human Normal and Cancerous Tissues

description: Circular RNAs (circRNAs) represent a novel class of widespread and diverse endogenous RNAs that may regulate gene expression in eukaryotes. However, the regulation and function of human circRNAs remain largely unknown. Here we generate ribosomal-depleted RNA sequencing data from six normal tissues and seven cancers, and detect at least 27,000 circRNA candidates. Overall design: RNA profiles of six normal tissues and seven cancers were generated by deep sequencing, using Illumina HiSeq 2000.
DOI: 10.26036/cnphis0002377
title: Phylogenomics of ants in the genus Acropyga, based on UCE sequences.

description: Acropyga are a world-wide clade of small subterranean formicine ants that live in obligate associations with root mealybugs. We used a data set of 944 loci of ultraconserved elements (UCEs) to reconstruct the phylogeny of 23 Acropyga species with both concatenation and species-tree approaches. The biogeographic history of the genus was investigated performing divergence dating analyses on 100 UCE loci and ancestral range reconstructions. The mutualism of Acropyga with their mealybug partners, as well as associated mandibular variation in the ants was reconstructed using methods of ancestral state reconstructions. We recovered a highly supported species phylogeny for Acropyga with both concatenation and species-tree analyses. The age for crown-group Acropyga is estimated around 30 Ma. Two main Acropyga lineages are recovered that are distributed mutually exclusive in the Old World and New World. Within the Old World clade, a Palearctic and African lineage is suggested as sister to the remaining species. Although present-day associations involve a number of mealybug genera, ancestral state reconstructions indicate that Old World species have diversified mainly in close association with xenococcines from the genus Eumyrmococcus. New World Acropyga predominantly evolved with Neochavesia until a recent (10-15 Ma) switch to rhizoecid mealybug partners (genus Rhizoecus). Overall, our results highlight the need for an extended investigation of the potential co-evolution of these ants with their mealybug partners.
DOI: 10.26036/cnphis0002378
title: Arabidopsis thaliana Genome sequencing and assembly

description: This study aims at characterizing the variation between the current strain genome of Arabidospsis thaliana and the second widely used strain Ler. We have assembled the genome of Ler to chromosome resolution using multiple data sources. Thus, we have revealed the complement of translocations and inversions at a population level.
DOI: 10.26036/cnphis0002379
title: Cucurbitaceae cultivar:Chinese long Transcriptome or Gene expression

description: Finite world rock phosphate (Pi) reserves will impose a major limitation on agricultural productivity and food security. Modern breeding programs are currently aimed at developing Pi-efficient crops having sustainable yields under reduced Pi fertilizer. In this regard, although the long-term response of plants to Pi stress is well documented, the early signaling events have yet to be elucidated. Here, we present studies showing that Pi, and the phytohormones, cytokinin and gibberellin function as root-to-shoot Pi stress signals that are perceived, in the shoot, by the vascular system. We further show that major changes occurred in the phloem mRNA population, and grafting studies revealed that thousands of mRNAs were delivered to specific sink tissues. Thus, the shoot vascular system acts as the site of root-derived Pi stress perception, and the phloem serves to deliver a cascade of signals to various sinks, presumably to coordinate Pi homeostasis at the whole-plant level.
DOI: 10.26036/cnphis0002380
title: SeqApiPop (Dataset 1)

description: A resequencing project to characterise the genetic diversity of honeybees throughout France.
DOI: 10.26036/cnphis0002382
title: Columbicola sp. Raw sequence reads

description: Columbicola genome sequencing project
DOI: 10.26036/cnphis0002383
title: Arabidopsis thaliana isolate:Col-0 Raw sequence reads

description: Improvement for PacBio full-length cDNA sequencing using Arabidopsis thaliana
DOI: 10.26036/cnphis0001691
title: Ectopistes migratorius Genome sequencing

description: Estimation of the population history of the passenger pigeon <i>Ectopistes migratorius</i>.
DOI: 10.26036/cnphis0001696
title: Public Health England - Salmonella

description: This BioProject contains the whole genome sequence data uploaded by the Salmonella Reference Service (Gastrointestinal Bacteria Reference Unit), Public Health England.
DOI: 10.26036/cnphis0001697
title: Transcriptome responses to dietary aflatoxin B1 exposure in domestic turkey

description: Dietary exposure to aflatoxin B1 (AFB1) can have severe negative impacts on poultry health and production. Domestic turkeys (Meleagris gallopavo) are especially sensitive to AFB1-induced hepatotoxicity and immunosuppression. In the turkey liver, AFB1 is efficiently activated by cytochrome P450 enzymes (P450s), but cannot be detoxified by alpha-class glutathione-S-transferase enzymes (GSTAs). The overall goals of our study were use RNA-sequencing (RNA-seq) to determine the impacts of AFB1 on the transcriptome in the turkey liver and spleen and evaluate the potential of a Lactobacillus-based probiotic (PB) to reduce aflatoxicity. Male Nicholas turkey poults were randomly divided into 4 treatment groups (CNTL, AFB, PB and PBAFB) and exposed to PB and/or AFB1 according to the protocols described in Monson et al., 2014. Tissue samples were collected for RNA extraction from 3 birds in each treatment upon completion of the challenge trial. Liver RNA samples were pooled by treatment before library construction (n=4 libraries), while spleen samples were run multiplexed as individual libraries (n=12 libraries). Libraries were sequenced on the Illumina GAII and the resulting single-end reads were de novo assembled into predicted transcripts for each tissue. BLAST annotation, differentially expression and functional analysis were used to determine the impacts of AFB1 and PB on expression in the liver and spleen. Candidate genes identified in these transcriptome analyses provide a resource for future research on AFB1 and efforts to increase the resistance of domestic turkeys.
DOI: 10.26036/cnphis0001698
title: Hippotragus niger variani Genome sequencing

description: Genomic resources for the critically endangered giant sable antelope.
DOI: 10.26036/cnphis0001699
title: Electrophorus electricus Genome sequencing

description: Genome sequence of Electrophorus electricus, the electric eel
DOI: 10.26036/cnphis0001700
title: Bacteriome metagenome of Tettigades auropilosa specimen TETAUR

description: Cicadas species are globally distributed and are important insects ecologically and economically. Their success depends upon amino acid providing bacteria that are harbored in specialized organs called bacteriomes. These bacteria have among the smallest genomes of any bacteria; how they function at a cellular level with such small genomes is unknown. To address this question, we sequenced the bacterial symbionts harbored by Cicada species from around the world.
DOI: 10.26036/cnphis0001701
title: Coturnix japonica Random survey

description: The sequence represents the genes expressed in three tissues from six sexually male Japanese quail (testis, foam gland, liver), which is a domesticated bird. Sequences derive from three different kinds of treatments -- males in breeding condition, males in winter condition, and males in winter condition that have been administered testosterone. This data set is useful to understand the evolution of male reproductive traits at the gene sequence level.
DOI: 10.26036/cnphis0002384
title: GenomeTrakr Project: Thakur Molecular Epidemiology Laboratory, NC State University

description: Whole genome sequencing of cultured Salmonella as part of the US Food and Drug Administration surveillance project for the rapid detection of outbreaks of foodborne illnesses.
DOI: 10.26036/cnphis0002385
title: Subantarctic Fur Seal (Arctocephalus tropicalis) and South American Fur Seal (Arctocephalus australis) virome

description: We provide the fecal virome of two species of fur seals: Arctocephalus tropicalis and Arctocephalus australis, collected from 10 specimens (A. tropicalis n=5; A. australis n=5).
DOI: 10.26036/cnphis0002386
title: Tamias alpinus Raw sequence reads

description: Raw sequence reads (Illumina HiSeq 2000 100PE) derived from Transcriptome-based exon captures.
DOI: 10.26036/cnphis0002387
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0002388
title: Expression data from adult mouse Nucleus Accumbens following prenatal infection

description: Prenatal exposure to infectious or inflammatory insults can increase the risk of neuropsychiatric disorders with neurodevelopmental components, including schizophrenia and autism. The molecular processes underlying this pathological association are only partially understood. Here, we implemented an unbiased genome-wide transcriptional profiling of the nucleus accumbens of mice exposed to prenatal infection on GD17 compared to control subjects in order to elucidate the long term molecular signature of late prenatal infection. We used microarray analysis to investigate the long lasting gene expression changes in a well-established mouse model that is based on maternal treatment with the viral mimic poly(I:C) during pregnancy Overall design: C57BL/6 mice were treated with the synthetic viral mimetic poly(I:C) (5 mg/kg, i.v.) or control (saline, i.v.) solution on gestation day 17. Offspring were subjected to cognitive and behavioral testing in adulthood, and then whole genome gene expression analysis with Affymetrix Microarray and subsequent q-PCR validation were performed on the nucleus accumbens.
DOI: 10.26036/cnphis0002389
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002391
title: Extinct birds and type specimens sequencing - Natural History Museum, University of Oslo.

description: In this project we have sequenced extinct birds and type specimens in the bird collection at the Natural History Museum, University of Oslo, aiming to reconstruct complete mitochondrial genomes. Genome sequencing and assembly.
DOI: 10.26036/cnphis0001702
title: The Gibbon Genome

description: Analysis of the gibbon genome provides a novel perspective on the accelerated chromosome evolution of small apes.
DOI: 10.26036/cnphis0001703
title: Whole genome sequencing-based benchmarking of subtyping methods for Salmonella enterica serotype Enteritidis

description: A total of 52 Salmonella enterica subspecies enterica serotype Enteritidis (SE) isolates representing 16 major outbreaks and three sporadic cases in the United States between 2001 and 2011 were sequenced and subjected to a retrospective investigation with a combination of four subtyping methods. Whole genome single nucleotide polymorphism typing (WGST) resolved all outbreak clusters and provided useful epidemiological information with robust phylogenetic inference. While both MLVA and CRISPR-MVLST yielded higher discriminatory power than PFGE, MLVA outperformed in delineating outbreak clusters whereas CRISPR-MVLST showed the potential to trace major lineages and ecological origins of SE. Our results suggested that whole genome sequencing (WGS) makes a viable platform for the evaluation and benchmarking molecular subtyping methods.
DOI: 10.26036/cnphis0001704
title: Mus musculus musculus strain:C57L/J Genome sequencing

description: The goal of this study was to obtain the complete genome sequence of the C57L/J in order to compare it to the C57BL/6J and identify variants that we could use for genetic mapping between the two strains.
DOI: 10.26036/cnphis0001705
title: Ancient homology underlies adaptive mimetic diversity across butterflies

description: Convergent evolution provides a rare, natural experiment with which to test the predictability of adaptation at the molecular level. Little is known about the molecular basis of convergence over macro-evolutionary timescales. Here we use a combination of positional cloning, population genomic resequencing, association mapping, and developmental data to demonstrate that positionally orthologous nucleotide variants in the upstream region of the same gene, WntA, are responsible for parallel mimetic variation in two butterfly lineages that diverged more than 65 million years of ago. Furthermore, characterization of spatial patterns of WntA expression during development suggests that alternative regulatory mechanisms underlie wing pattern variation in each system. Taken together, our results reveal a strikingly predictable molecular basis for phenotypic convergence over deep evolutionary time.
DOI: 10.26036/cnphis0001706
title: Polyadenylated RNA Sequencing of C57BL/6J Embryonic, Adult and Pressure-Overloaded Hearts

description: A few reports have implicated specific lncRNAs in cardiac development or failure, but precise details of lncRNAs expressed in hearts and how their expression may be altered during embryonic heart development or by adult heart disease is unknown. By comparing lncRNA profiles of normal embryonic (~E14), normal adult, and hypertrophied adult hearts we defined a distinct fetal lncRNA abundance signature that includes 157 lncRNAs differentially expressed compared to adults (fold-change = 50%, FDR=0.02), and which was only poorly recapitulated in hypertrophied hearts (17 differentially expressed lncRNAs; 13 of these observed in embryonic hearts). Analysis of protein-coding mRNAs from the same samples identified 22 concordantly and 11 reciprocally regulated mRNAs within 10 kb of dynamically expressed lncRNAs, reciprocal relationships of lncRNA and mRNA levels was validated for the Mccc1 and Relb genes using in vitro lncRNA knockdown in C2C12 cells. Network analysis suggested a central role for lncRNAs in modulating NFkappaB- and CREB1-regulated genes during embryonic heart growth and identified multiple mRNAs within these pathways that are also regulated, but independently of lncRNAs. Overall design: Cardiac polyadenylated RNA (mRNA and lncRNA) profiles were generated from C57BL/6J mouse hearts were generated on Illumina HiSeq 2000 instruments. 7 independent E13.5 hearts, 12 adult hearts (6 at 6 weeks of age, 6 at 16 weeks of age), 4 sham-operated hearts at 12 weeks of age, and 4 hearts after 4 weeks of pressure overload (TAC) at 12 weeks of age.
DOI: 10.26036/cnphis0001707
title: Echis coloratus Genome sequencing

description: Genome sequencing of the painted saw-scaled viper (Echis coloratus) for use in studies focusing on snake venom evolution and vertebrate genome evolution
DOI: 10.26036/cnphis0001708
title: National Institute of Standards and Technology microbial genomic DNA reference material sequence data

description: Data from the sequencing experiments used to characterize the NIST microbial genomic DNA reference materials.
DOI: 10.26036/cnphis0001709
title: Florida Manatee Gastrointestinal Tract Targeted Locus (Loci)

description: Florida Manatee Gastrointestinal tract microbiome
DOI: 10.26036/cnphis0002390
title: Bison bonasus breed:Lowland Bialowieza line Genome sequencing

description: The goal of this project is to infer the demographic and adaptive histories of the wisent (Bison bonasus) also known as European bison, from individual whole genome sequencing data.
DOI: 10.26036/cnphis0002392
title: Whitefly (Bemisia tabaci) MEAM1 genome sequencing

description: Whiteflies are among the most important insect pests and plant virus vectors. We sequenced and de novo assembled the genome of the whitefly Bemisia tabaci, Middle East-Asia Minor 1 (MEAM1), which provides a valuable resource to help understand unique features of whiteflies and develop novel strategies to manage whiteflies and the viruses they transmit.
DOI: 10.26036/cnphis0002393
title: Hummingbird Genomics and Evolution (HuGE)

description: This is an international collaborative effort to illuminate hummingbird evolution by developing genome sequences for comparative analysis. Key goals include studying phylogeny and molecular evolution of this charismatic clade, especially as they relate to biogeography, local adaptation, ecophysiology, and conservation biology.
DOI: 10.26036/cnphis0002394
title: Pyrus communis Transcriptome or Gene expression

description: The high-throughout sequencing data of seven key fruit developmental stages, from fruit setting to maturation and fruit senescence after harvesting will help to further study of fruit quality, and builds models for gene-expression for fruit development from different species of pear, even Rosaceae.
DOI: 10.26036/cnphis0002396
title: Diversity of Salmonella enterica serovar Typhimurium recently isolated in the U.S.

description: Each year non-typhoidal Salmonellae cause an estimated 1.2 million illnesses in the U.S., 80 million illnesses globally, from contaminated food or water. Typhimurium is one of the most common serovars associated with foodborne outbreaks, causing self-limiting gastroenteritis, and in approximately 5% of infected patients systemic infection. Strain diversity and genetic factors contributing to differential human pathogenicity are poorly understood. This study was carried out to assess the diversity of S. Typhimurium recently isolated in the U.S. and to place U.S. strains in a global context.
DOI: 10.26036/cnphis0002397
title: Hybrids of Hypophthalmichthys molitrix and H. nobilis raw sequence reads

description: Sympatric bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) (Asian carps) remain genetically isolated within their native ranges, but have rampantly hybridized when introduced into the novel Mississippi River Basin environment.
DOI: 10.26036/cnphis0002399
title: Hypophthalmichthys nobilis Raw sequence reads

description: to constructe high density genetic map for bighead carp
DOI: 10.26036/cnphis0002400
title: Anas platyrhynchos Raw sequence reads

description: research the origin of the domestic ducks
DOI: 10.26036/cnphis0001710
title: Watasenia scintillans strain:Namerikawa Genome sequencing

description: The complete genome sequence of the mitochondrial DNA of the sparkling enope squid was determined using the Illumina sequencing platform.
DOI: 10.26036/cnphis0001711
title: Microplitis demolitor strain:Queensland-Clemson subculture Genome sequencing and assembly

description: Microplitis demolitor genome.
DOI: 10.26036/cnphis0001712
title: Wheat (Triticum aestivum L.) transcriptome profiling

description: Transcript changes in response to low temperature Overall design: Total RNA for RNA-seq analysis were extracted from wheat leaf tissues with three biological replicates for each growth condition.
DOI: 10.26036/cnphis0001713
title: Molgula occidentalis, M. occulta, and M. oculata genome samples

description: The goals of the study are to understand the molecular underpinnings of embryonic development in Molgula species. This is relevant to understanding basic mechanisms of chordate development and to the study of gene regulatory networks in general.
DOI: 10.26036/cnphis0001714
title: Exome sequencing of gastric cancer-derived ascites

description: Profiles of somatic mutations in gastric cancer peritoneal metastases
DOI: 10.26036/cnphis0001715
title: Anser cygnoides isolate:SCWG-2014 Genome sequencing and assembly

description: We sequenced the transcriptome in the hypothalamus and ovary and hypophysis of the Sichuan white goose using Illumina MiSeq to determine differentially expressed genes during the prelaying and laying periods and to provide a comprehensive analysis of gene expression profiles in the hypothalamus of the Sichuan white goose.
DOI: 10.26036/cnphis0001717
title: Metagenomic analysis of rat intestinal microflora

description: Regionally distinct alterations in the composition of the gut microbiota in streptozotocin- induced diabetic rats.
DOI: 10.26036/cnphis0001718
title: Schizothorax richardsonii Transcriptome or Gene expression

description: Heat shock response of Schizothorax richardsonii
DOI: 10.26036/cnphis0002401
title: Raw sequence reads of Angiostrongylus cantonensis

description: Developmental transcriptomes of young adults (L5) and female (F) were built by RNA-seq to establish sequence background of A.cantonensis for discover genes responsible for high speed growth and other events.
DOI: 10.26036/cnphis0002402
title: Felis catus Raw sequence reads

description: 99 Lives Cat Genome Sequencing Initiative. This project proposes to sequence 99 cats to support health care for the normal household cat and fancy cat breeds too. In this experiment, RNA sequencing was performed across a variety of animals and tissues in order to improve gene annotation in the cat.
DOI: 10.26036/cnphis0002403
title: Ixodes scapularis Genome sequencing

description: Genomic sequencing of a pool of ten Ixodes scapularis looking for the presence of borrelia burgdorferi
DOI: 10.26036/cnphis0002404
title: Eucommia ulmoides Raw sequence reads

description: ucommia ulmoides Oliver, the only member of the Eucommiaceae family, is a rare and valuable tree endemic to China. The species has been widely planted for vegetable oilproduction, the oil from the kernels of E. ulmoides contains various fatty acids, especially rich in a-linolenic acid (ALA), which constitutes as much as 60% of the total fatty acids.
DOI: 10.26036/cnphis0002406
title: Salvelinus namaycush Raw sequence reads

description: The main goal of this study was to investigate the extent of parallelism in the genomic and phenotypic divergence between piscivorous and planktivorous Lake Trout ecotypes from Laurentian Shield lakes.
DOI: 10.26036/cnphis0002407
title: Giraffa camelopardalis tippelskirchi, Okapia johnstoni Genome sequencing and assembly

description: The goal of this project was to sequence the genomes of giraffe and okapi to provide the necessary information to conduct a comparative genomics analysis between giraffe and okapi and among other mammals for the purpose of identifying genetic changes in giraffe responsible for its unique morphological and physiological characters. Okapi is a particularly useful comparison as it is closely related to giraffe but lacks giraffe unique features.
DOI: 10.26036/cnphis0001716
title: Felis silvestris silvestris strain:Scottish wildcat Genome sequencing

description: Felis silvestris silvestris whole-genome sequencing.
DOI: 10.26036/cnphis0001719
title: Anopheles gambiae male and female sequencing

description: None