cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0001813
title: Salmonella enterica subsp. enterica serovar Enteritidis Genome sequencing

description: Whole genome sequencing to characterize an important and prevalent foodborne pathogen
DOI: 10.26036/cnphis0001814
title: Glycine strain:Glycine.max and Glycine.soja Genome sequencing

description: Soybean resequencing data
DOI: 10.26036/cnphis0001815
title: Human gut Targeted Locus (Loci)

description: Gut microbiota has been causatively linked with diet-induced obesity; however, its role in human genetic obesity remains elusive. Here we used bar-coded pyrosequencing of 16S rRNA gene V1-V3 region to show that dietary modulation of a structurally and functionally imbalanced gut microbiota significantly alleviates morbid obesity in children with Prader-Willi Syndrome.
DOI: 10.26036/cnphis0001816
title: Mouse lemur reference genome and diversity panel.

description: The BCM-HGSC is sequencing and assembling the genome of the gray mouse lemur (Microcebus murinus). A high quality draft sequence of the reference genome will be assembled from a female mouse lemur, using read data produced by the Illumina platforms. The BCM-HGSC is currently generating deep Illumina read coverage from the same animal that was previously used by the Broad Institute to generate approximately 2x Sanger sequence coverage. The BCM-HGSC is also using the Pacific Biosciences RS platform to generate several-fold coverage of long reads that will be used to close gaps in the initial Illumina-based assembly. The BCM-HGSC is collaborating in this project with Dr. Anne Yoder of the Duke Lemur Center. The reference animal was obtained from the DLC mouse lemur colony. A BioNano map of a lemur genome was deposited as SUPPF_0000000066, and links to those files are present in ftp://ftp.ncbi.nlm.nih.gov/pub/supplementary_data/bionanomaps.csv In addition to the deep sequence coverage of the reference mouse lemur, BCM-HGSC will generate whole genome sequences from additional mouse lemurs, both to identify DNA sequence variation within Microcebus murinus and to characterize genomic differences among species within this genus. Additional samples from M. murinus have been obtained from Anne Yoder (DLC) and Dr. Corrine Lautier,Universit Montpellier II, France. Analyses will include comparisons with the human and other nonhuman primate genomes. Mouse lemurs are members of the Family Cheirogaleidae, strepsirrhine primates that diverged from the ancestors of humans and apes more than 50 million years ago. The genus Microcebus is endemic to Madagascar, and consists of at least 12 recognized species. M. murinus, the gray mouse lemur, is nocturnal with small body size (55-65 grams) and complex social behavior. Mouse lemurs provide important comparative genomic information for analyses of the evolution of the human and other primate genomes. As strepsirrhine primates, they serve as an outgroup to all comparisons among New World monkeys, Old World monkeys, apes and humans. Mouse lemurs are also used as animal models for various studies related to human biology and disease, including aging, reproductive biology and Alzheimer''s disease.
DOI: 10.26036/cnphis0001817
title: Eurasian Siskin (Carduelis spinus) Blood Transcriptome

description: Eurasian siskins experimentally infected with avian malaria, as well as uninfected individuals, in order to evaluate the avian transcriptome response to malaria.
DOI: 10.26036/cnphis0000421
title: Capra hircus Raw target enrichment sequence reads

description: We propose to design a goat SNP chip using the SHS-based target enrichment strategy. This chip was further tested in a genome-wide association analysis of cashmere fineness (fiber diameter). These are the whole-genome sequencing data of 436 cashmere goats.
DOI: 10.26036/cnphis0000422
title: Macaca mulatta Targeted Locus (Loci)

description: analysis the t- and b-lymphocyte receptor repertoires
DOI: 10.26036/cnphis0000423
title: Cleome hassleriana Genome sequencing

description: We report upon the genome sequence of Cleome using Next-generation sequencing platform, resulting in about 139X genome coverage by paired short read sequences from different insert size libraries. The final assembly combined the denovo method with a high-quality physical map based on an 8X Whole Genome Profiling of a BAC-library, producing a 273Mb genome (94% of the estimated 290 Mb genome size).
DOI: 10.26036/cnphis0000424
title: CompleteGenomics sequencing of (PUR) Puerto Rican in Puerto Rico

description: -
DOI: 10.26036/cnphis0000425
title: CompleteGenomics sequencing of (KHV) Kinh in Ho Chi minh City, Vietnam

description: -
DOI: 10.26036/cnphis0000426
title: The 100-Person Wellness Project (HPWP)

description: 108 individuals (age 21-89+ years; 59% males, 41% females; 89% Caucasian; not recruited based on any specific phenotype) participated in an IRB-approved study from April 2014 to January 2015. Each individual had the genome sequenced in full. Blood was collected in clinics every three months. Additionally, participants completed at-home collections of saliva, stool, and first morning void urine every three months. Stool and saliva samples were shipped directly to the vendor by the participant, while urine was given back to the study coordinators for distribution to the proper sample vendor. For each successful participant in each round we carried out 218 clinical laboratory tests, measured up to 643 metabolites and 262 proteins, and measured the abundance of 4616 operational taxonomic units (OTUs) in the gut microbiome using 16S rRNA sequencing. The P100 study had four objectives: 1) Establish cost-efficient procedures for generating, storing and analyzing... (for more see dbGaP study page.)
DOI: 10.26036/cnphis0000427
title: Acanthopagrus schlegelii Raw sequence reads.SRP112710

description: Genome andTranscriptome analysis of Acanthopagrus schlegeli
DOI: 10.26036/cnphis0000428
title: Brassica oleracea genome sequencing

description: The objectives of this study to provide Brassica oleracea genome sequence and relevant information such as gene annotation and genome structure, analyze evolution of the genome structure and pathways, and explore related genes controling the species characteristics.
DOI: 10.26036/cnphis0000429
title: Lasioglossum albipes Genome sequencing and assembly

description: Whole genome de novo sequencing of Lasioglossum albipes.
DOI: 10.26036/cnphis0001137
title: Integration of transcriptome and proteome of duck liver in response to DHAV-C

description: These data provide useful information for future facilitate the duck genome information. The identified differentially expressed unigenes, miRNA and proteins provide new insights into better understanding the molecular mechanism of host- DHAV-C interaction and a clue for the discovery of some new genes associated with infection.
DOI: 10.26036/cnphis0001138
title: Camelus ferus Genome sequencing

description: The genome sequences and analysis of wild and domestic bactrian camels. Bactrian camels, or two-humped camels (Camelus bactrianus), are large and charismatic animals, providing important production and transportation tools for people of cold desert regions in China and Mongolia. The genomic information will serve a critical need and trigger research, conservation and utilization in the camel family.
DOI: 10.26036/cnphis0001139
title: Genetic Programs in Human and Mouse Early Embryos Revealed by Single-Cell RNA-Sequencing

description: Mammalian preimplantation development is a complex process involving dramatic changes in the transcriptional architecture. Through single-cell RNA-sequencing (RNA-seq), we report here a comprehensive analysis of transcriptome dynamics from oocyte to morula in both human and mouse embryos. Based on single nucleotide variants (SNVs) in blastomere mRNAs and paternal-specific SNPs, we identify novel stage-specific monoallelic expression patterns for a significant portion of polymorphic gene transcripts (25-53%). By weighted gene co-expression network analysis (WGCNA), we find that each developmental stage can be concisely delineated by a small number of functional modules of co-expressed genes. This result indicates a sequential order of transcriptional changes in pathways of cell cycle, gene regulation, translation, and metabolism in a step-wise fashion from cleavage to morula. Cross-species comparisons reveal that the majority of human stage-specific modules (7 out of 9) are remarkably preserved, only to diverge in developmental specificity and timing in mice. We further identify conserved key members (or hub genes) of the human and mouse networks. These genes represent novel candidates that are likely key players in driving mammalian preimplantation development. Collectively, we demonstrate that mammalian preimplantation development is orchestrated by evolutionarily conserved genetic programs that diverge in developmental timing. Our results provide a valuable resource to dissect gene regulatory mechanism underlying progressive development of early mammalian embryos. Overall design: single-cell RNA-seq of human and mouse blastomeres
DOI: 10.26036/cnphis0001140
title: Stomoxys calcitrans Genome sequencing and assembly

description: The stable fly Stomoxys calcitrans is an obligate blood feeder, closely related to tetse fly. S. calcitrans is a mechanical vector of typanosomes but unlike tetse, it does not transmit disease-causing parasites to humans. Genomic data from this organism will contribute to the understanding of vector competence in tetse fly and the transmission of trypanosomiasis.
DOI: 10.26036/cnphis0001818
title: Aedes aegypti subspecies Genome sequencing

description: To gain insight into evolution and sex-determination mechanisms in Aedes aegypti, genomic exome capture libraries from representative collections, from Senegal and other locations, were sequenced and analyzed to identify single nucleotide polymorphisms (SNPs). West African and Thai collections included comparisons between males and females. Thai female replicate libraries: SRS682692 and SRS682687 (Ox10, Ox12); Thai male replicates: SRX679429 and SRX679427 (Ox09, Ox11). PK10 female replicates: SRX679424 and SRX679426 (Ox02, Ox04); PK10 male replicates: SRX679423 and SRX679425 (Ox01, Ox03).
DOI: 10.26036/cnphis0001819
title: Apis dorsata Genome Sequencing Project

description: Giant Honeybee (Apis dorsata) genome sequencing project.
DOI: 10.26036/cnphis0001820
title: Bombus impatiens genome sequencing project

description: <i>Bombus impatiens</i> is the #2 pollinator in the United States. The genome was sequenced by the Biotechnology Center, University of Illinois (BCUI), using genomic DNA from haploid males. The assembly was done by the Center for Bioinformatics and Computational Biology at University of Maryland.
DOI: 10.26036/cnphis0001821
title: Buchnera aphidicola (Aphis glycines) strain:BAg Genome sequencing

description: The purpose of this study is three-fold: 1) sequence and assemble the genome sequence of Buchnera aphidicola in the soybean aphid, A. glycines; 2) conduct a phylogenetic analysis to examine the similarity of the soybean aphid Buchnera with the Buchnera characterized in other aphid species; and 3) assess sequence variation in the Buchnera between different soybean aphid biotypes. These results will provide a foundation for assessing how the aphid microflora influences plant resistance.
DOI: 10.26036/cnphis0000430
title: Brassica napus Raw sequence reads

description: The raw sequencing reads of Brassica napus cultivar ''ZS11'' resulted from whole-genome shotgun (WGS) methods.
DOI: 10.26036/cnphis0000431
title: Homo sapiens (human blood) Genome sequencing

description: The genome sequence data of NIPD trio #1, including the genome sequencing of the father (PB), mother (blood cell), the offspring (cord blood) and the maternal plasma at GW of 13.
DOI: 10.26036/cnphis0000432
title: Pyrus x bretschneideri Genome sequencing and assembly

description: Pear (Pyrus spp.) is one of the leading cultivated fruit trees of temperate regions, and grown widely in all the continents of the world. Here we present a high-quality draft genome sequence assembly of Pyrus bretschneideri Rehd. Var. Dangshansuli, sequenced with 7.6X coverage, and demonstrate that a highly heterozygous plant genome can be assembled using a novel combination of BAC-by-BAC strategy and next generation sequencing without physical reference.
DOI: 10.26036/cnphis0000433
title: Myotis brandtii Genome sequencing and assembly

description: Whole genomic sequence and analysis of Myotis brandtii.
DOI: 10.26036/cnphis0000434
title: Populus euphratica strain:callus Genome sequencing and assembly

description: Poplars have been used as the model forest species for diverse studies not only because of their relative eases of experimental and genetic manipulation but also due to their economical and ecological importance.
DOI: 10.26036/cnphis0000435
title: Desmodus rotundus isolate:DRU21DN04 Genome sequencing and assembly

description: Common vampire bat genome sequencing and assembly
DOI: 10.26036/cnphis0000436
title: Cajanus cajan Genome Sequencing

description: Genome sequencing project from BGI
DOI: 10.26036/cnphis0000437
title: Single cells Genome Sequencing-1

description: The pilot study on single cell CNV detection in BGI-Shenzhen. Single cells isolated from blood or embryos.
DOI: 10.26036/cnphis0000438
title: Metagenomic sequencing of the gut microbiomes of bats with different diets

description: Metagenomic sequencing of the gut microbiomes of bats with different diets derive from Rousettus aegyptiacus (frugivorous), Macroderma gigas (carnivorous), Rhinolophus ferrumequinum (insectivorous), and Desmodus rotundus (sanguivorous).
DOI: 10.26036/cnphis0001141
title: Triticum aestivum strain:Chinese spring deletion line Random survey

description: This experiment was designed to assist chromsome-arm-specific sequencing and assembly of Triticum aestivum. DNA was isolated from cytogenetic stock with a deletion of chromosome arms to produce chromosome arm DNA.
DOI: 10.26036/cnphis0001142
title: Daubentonia madagascariensis Genome sequencing

description: Whole genome sequences for 13 Daubentonia madagascariensis (aye-aye) individuals.
DOI: 10.26036/cnphis0001143
title: Cooperia oncophora Genome Sequencing

description: The Genome Institute and collaborators are sequencing the intestinal worm, Cooperia oncophora. One of the Trichostrongylids, it is an economically important gastrointestinal parasite of sheep, goats and other ruminants worldwide. Control of members of this genus has become difficult worldwide due to widespread drug resistance to all major classes of anthelmintic. This group has arguably been the subject of a substantial research effort on vaccine and diagnostic test development, control strategies, drug efficacy trials and drug resistance. Some species are important models of parasitism as well as important pathogens. Trichostrongylus species are of major veterinary and economic importance, causing substantial production losses (through a reduction in weight gain, meat and/or milk production) to farmers and exacerbating the global food shortage problem. Of most importance are the parasites of grazing livestock, which cause significant economic problems to agriculture and detrimental effects on animal welfare. The trichostrongylid nematodes were ranked as a group (since they mainly occur as mixed infections) and were top of that list (i.e. considered to have a greater impact than any other disease of domestic animals). This group of parasites is also amongst the most economically important diseases of livestock in the developed world.
DOI: 10.26036/cnphis0001144
title: Ostertagia ostertagi Genome Sequencing

description: The Genome Institute and collaborators are sequencing the bovine stomach worm, Ostertagia ostertagi. This is the most economically important parasite of cattle throughout temperate regions of the world. Globally, these small reddish brown worms are the major cause of parasitic gastritis (Ostertagiosis) of ruminants. The worms embed themselves in the lining of the cow''s fourth stomach causing decreased acid production, loss of appetite, diarrhea, weight loss and even death. O.ostertagi infections can prompt protective immunity to ostertagiosis, making the species a good candidate for vaccine development. Having a whole genome sequence for the species could also help with the development of novel methods to control these parasites in livestock, including defining the mechanisms underlying drug susceptibility and resistance with the possibility of extending the useful life of existing drugs and improving diagnostics in this area, as well as providing the means to study the host-parasite interaction in whole animals.
DOI: 10.26036/cnphis0001145
title: Whole genome sequences for a set of 79 great ape individuals. Genome sequencing

description: A set of sequencing files for four great ape species. Chimpanzee, Bonobo, Gorilla and Orangutan.
DOI: 10.26036/cnphis0001146
title: Drosophila malerkotliana malerkotliana strain:mal0-isoC Genome sequencing

description: Genome sequencing of Drosophila malerkotliana malerkotliana.
DOI: 10.26036/cnphis0001147
title: Transcriptome resource of Chinese Tan sheep skin tissue

description: This data provides Transcriptome sequences from skin tissues of four Chinese Tan sheep. This study provides some clues for elucidating the molecular mechanism of phenotype change with age in Chinese Tan sheep, as well as supplying some potential values for understanding human hair loss and texture changes.
DOI: 10.26036/cnphis0001148
title: Pseudopodoces humilis Phenotype or Genotype

description: Research origin and evolution
DOI: 10.26036/cnphis0001149
title: Guillardia theta CCMP2712 Transcriptome or Gene expression

description: Guillardia theta CCMP2712 Transcriptome.
DOI: 10.26036/cnphis0001822
title: Milnesium tardigradum Genome sequencing

description: The genome of M. alpigenum is targeted for evolutionary analysis and comparative studies with other Metazoa species. Special focus is the phylogenetic positioning of the tardigrades and anhydrobiosis-related genome features.
DOI: 10.26036/cnphis0001823
title: Individuality and variation of personal regulomes in human T cells

description: We surveyed the variation and dynamics of active regulatory elements genome-wide in CD4+ T cells, using Assay of Transposase Accessible Chromatin with sequencing (ATAC-seq) in longitudinal samples from healthy volunteers and during T cell activation. We created robust pipelines that enable accurate single molecule counting and allelic discrimination from clinical material. Over 4000 regulatory elements (7.2%) showed reproducible personal variation in activity. Gender was the most significant attributable source of regulome variation. ATAC-seq revealed novel elements that escape X chromosome inactivation and predicted gender-specific gene regulatory networks across autosomes, which coordinately impact genes with immune function. Noisy regulatory elements with personal variation in accessibility are significantly enriched for autoimmune disease loci. Over one third of regulome variation lacked genetic variation in cis, suggesting contributions from environmental or epigenetic factors. These results refine concepts of human individuality and provide foundational reference to compare disease-associated regulomes. Overall design: We examined chromatin structure using ATAC-seq in purified human CD4+ T cells in 33 samples from 12 healthy donors and 15 samples from 3 patients with cutaneous T cell leukemia (CTCL). For T cell activation (TCA) time course, CD4+ cells from healthy donor 1 isolated as above were stimulated with ionomycin (1 ug/mL) and Phorbol Myristate Acetate (PMA; 20 ng/mL) and collected at 0, 1, 2, 4 hours in duplicate.
DOI: 10.26036/cnphis0001824
title: Polypodium hydriforme Genome sequencing

description: Polypodium hydriforme is an enigmatic cnidarian parasite of acipenseriforme fishes. This genome was sequenced in order to confirm the cnidarian affinity of P. hydriforme as well as to facilitate the discovery of developmental genes and other candidate genes that can help us understand the evolution of this taxon.
DOI: 10.26036/cnphis0001825
title: Zeugodacus cucurbitae strain:USDA-PBARC White Pupae T1 Genome sequencing and assembly

description: Whole genome sequencing of Bactrocera curcurbitae
DOI: 10.26036/cnphis0001826
title: Fopius arisanus strain:USDA-PBARC FA_bdor Genome sequencing and assembly

description: Whole genome sequencing of Fopius arisanus
DOI: 10.26036/cnphis0001827
title: Soil sample

description: A field study was conducted to compare bacterial communities of rhizosheaths of wheat grown under wheat-cotton and wheat-rice rotation and to study the effects of PGPB inoculation.
DOI: 10.26036/cnphis0001828
title: Paralichthys olivaceus Transcriptome or Gene expression

description: To find cold-related genes using RNA-seq.
DOI: 10.26036/cnphis0001829
title: Pig-tailed Macaque reference genome and diversity panel

description: A high quality draft sequence of the reference genome will be assembled from a single pig-tailed macaque, using read data produced by the Illumina platform. In addition to the deep genome sequence coverage for the reference animal, BCM-HGSC will generate whole genome sequences from additional individuals in order to identify DNA sequence variation for this species.
DOI: 10.26036/cnphis0001830
title: Amyelois transitella strain:UIUC subculture of SPIRL-1966 Genome sequencing and assembly

description: Amyelois transitella genome
DOI: 10.26036/cnphis0000439
title: Dugesia japonica Transcriptome or Gene expression

description: It is a model organism for studying the role of miRNAs in stem cell function. Next generation sequencing technology was used to identify the miRNAs of D. japonica. Bioinformatic analysis showed that 262 miRNA and miRNA* sequences were discovered, of which 102 miRNAs were the same as Schmidtea mediterranea (S. mediterranea) and 160 miRNAs were related to other animals. To identify the functional small RNAs during planarian regeneration, we collected 5 sample, which were whole body, head part, tail part, left part and right part of planarians. Each sample needed about 50 planarians and they were collected from a mountain creek in Zibo, Shandong Province.
DOI: 10.26036/cnphis0000440
title: T2D-GENES Project 2: San Antonio Mexican American Family Studies

description: The Type 2 Diabetes (T2D) Genetic Exploration by Next-generation sequencing in Ethnic Samples (T2D-GENES) Consortium is a collaborative international effort to identify genes influencing susceptibility to type 2 diabetes in multiple ethnic groups using next generation sequencing. T2D-GENES Project 2 (San Antonio Mexican American Family Studies [SAMAFS], Substudy 2) is a complex pedigree-based study designed to identify low frequency or rare variants influencing susceptibility to T2D. It uses whole genome sequence (WGS) information from 1,043 individuals in 20 Mexican American T2D-enriched pedigrees from San Antonio, Texas. The major objectives of this study are to identify low frequency or rare variants in and around known common variant signals for T2D, as well as to find novel low frequency or rare variants influencing susceptibility to T2D. The sampled individuals are obtained from two of the four SAMAFS: the San Antonio Family Heart Study (SAFHS)... (for more see dbGaP study page.)
DOI: 10.26036/cnphis0000441
title: Homo sapiens Genome sequencing.SRP017787

description: Nature Publishing Group.
DOI: 10.26036/cnphis0000442
title: Triticum aestivum Transcriptome or Gene expression

description: Triticum aestivum RNA seq.
DOI: 10.26036/cnphis0000443
title: Rice Field Eel Genome Sequencing

description: Whole genome sequence project.
DOI: 10.26036/cnphis0000444
title: Homo sapiens Transcriptome or Gene expression.SRP018008

description: We sequenced the RNA of 42 bladder cancer patients.
DOI: 10.26036/cnphis0000445
title: F1RT Metagenome

description: Metacellulosomics-driven discovery of bacterial synergism in a soil-derived cellulose-degrading community.