cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0000741
title: Permafrost metagenome

description: The fate of the carbon stocked in permafrost soils following global warming and permafrost thaw is of major concern in view of the potential for increased CH4 and CO2 emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but their composition and functional potential in permafrost soils are largely unknown. A 2m deep permafrost and its overlying active layer soil were subjected to metagenome sequencing, quantitative PCR, and microarray analyses. The active layer soil and 2m permafrost soil microbial community structures were very similar, with Actinobacteria being the dominant phylum. The two soils also possessed a highly similar spectrum of functional genes, especially when compared to other already published metagenomes. Key genes related to methane generation, methane oxidation and organic matter degradation were highly diverse for both soils in the metagenomic libraries and some (e.g. pmoA) showed relatively high abundance in qPCR assays. Genes related to nitrogen fixation and ammonia oxidation, which could have important roles following climatic change in these nitrogen-limited environments, showed low diversity but high abundance. The 2m permafrost soil showed lower abundance and diversity for all the assessed genes and taxa. Experimental biases were also evaluated and showed that the whole community genome amplification technique used caused large representational biases in the metagenomic libraries. This study described for the first time the detailed functional potential of permafrost-affected soils and detected several genes and microorganisms that could have crucial importance following permafrost thaw. Sequences deposited into the Sequence Read Archive can be found using the Project data link.
DOI: 10.26036/cnphis0000742
title: Mayetiola destructor genome sequencing project

description: The Mayetiola destructor genome has been sequenced by the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC).
DOI: 10.26036/cnphis0000743
title: Apis florea genome sequencing project

description: The <i>Apis florea</i> genome is being sequenced by the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) using NextGen sequencing. The genomic DNA for this project was isolated from a single haploid male.
DOI: 10.26036/cnphis0000744
title: Necator americanus causes Hookworm disease in humans

description: A draft assembly of the <i>Necator americanus</i> genome sequence is expected.
DOI: 10.26036/cnphis0000746
title: genomic sequence of DNA derived from a single CHO cell line.

description: None
DOI: 10.26036/cnphis0001438
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001439
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001440
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001441
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001442
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001443
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001444
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001445
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001446
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002125
title: Lolium perenne Raw sequence reads

description: discover the tolerance genes response to temperature stress
DOI: 10.26036/cnphis0002126
title: Festuca arundinacea Raw sequence reads

description: mining tolerance gene from tall fescue response to temperature stress
DOI: 10.26036/cnphis0002127
title: Leptoxis ampla Genome sequencing

description: High-throughput sequencing for obtaining a full mitochondrial DNA sequence of Leptoxis ampla
DOI: 10.26036/cnphis0002128
title: Felis chaus Genome sequencing

description: whole genome sequencing of Felis chaus
DOI: 10.26036/cnphis0002129
title: Felis margarita Genome sequencing

description: whole genome sequencing of Felis margarita
DOI: 10.26036/cnphis0002130
title: Prionailurus bengalensis Genome sequencing

description: whole genome sequencing of Prionailurus bengalensis
DOI: 10.26036/cnphis0002131
title: Nicrophorus vespilloides Genome sequencing and assembly

description: N. vespilloides is used as a model species for the evolutionary study of complex social behaviors; such as, parental care, sibling competition, and social competition. In sequencing, assembling, and analyzing the genome, we hoped to make this species genetically tractable to open questions about the molecular underpinnings of the behaviors of interest. We also characterized if there was DNA methylation in this beetle.
DOI: 10.26036/cnphis0002132
title: Perilla frutescens var. frutescens Transcriptome or Gene expression

description: Transcriptome analysis of oil plant Perilla frutescens (L.) var. frutescens and identification of genes related to ?-3 fatty acid biosynthesis
DOI: 10.26036/cnphis0002133
title: Macrostomum lignano strain:DV1 | isolate:DV1 Genome sequencing and assembly

description: Whole genome sequencing of Macrostomum lignano was done with Pacific Biosciences as well as Illumina devices. The project goal was to assemble the genome sequence.
DOI: 10.26036/cnphis0002134
title: Cricetomys gambianus Genome sequencing

description: Genome sequence of the Gambian pouched rat (Cricetomys gambianus)
DOI: 10.26036/cnphis0000747
title: Myzus persicae genome sequencing project

description: The <i>Myzus persicae</i> genome is being sequenced by the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) using the Illumina sequencing platform. The genomic DNA for this project was isolated from whole adults from a USDA tobacco adapted lineage (red).
DOI: 10.26036/cnphis0000748
title: Human Microbiome Project (HMP) Metagenomic WGS Projects, deeper sequencing of the human microbiome samples: Production Phase

description: The HMP metagenomes production phase represents the shotgun sequencing of metagenomic DNA extracted from samples taken from multiple body sites across hundreds of human subjects. Coupled with the other data generated during the HMP project, these results will provide insights into the genes and pathways present in the human microbiome. We are learning more and more about the ways that human health is influenced by the complex and dynamic communities of microbes (the human microbiota) present on and within our bodies. Disruptions in these communities may trigger or influence the course of various disease states. Preliminary studies have shown this to be the case for certain diseases. The Human Microbiome Project expands on these studies to better understand, prevent and treat many human diseases.
DOI: 10.26036/cnphis0000749
title: Felis catus

description: The DNA for this project came from the following sources:<br><pre> Name Breed Reads <br> Pixel Burmese 331,813<br> Zeelie Persian 298,332<br> Tipper Cornish Rex 272,607<br> Scooter Ragdoll 298,409<br> Speedy Domestic Shorthair 310,364<br> Cocoa Siamese 293,712<br> Felix African wild cat 1,373,060<br> Cinnamon Abyssinian 8,186,934<br></pre> This assembly adds 0.9X coverage to the 1.9X coverage of cinnamon assembly (ANG00000000). The 0.9X coverage comes from six other breeds and one wild cat from paired-end fosmid ABI 3730 reads. All 2.8X coverage was assembled and mapped to the cat genome as described in the 1.9X cat genome publication. The primary goal of this project is to discover SNPs, however, the assembly was a necessary step, and should prove quite useful to the research community.
DOI: 10.26036/cnphis0000750
title: The DNA methylome of human peripheral blood mononuclear cells

description: DNA methylation plays a vital role in genome dynamics and, in the human genome, occurs predominantly at cytosine guanine dinucleotide (CpG) sites. The diploid haploid human genome analysed here contains around 2060 million CpG sites (methylome) where DNA methylation can vary, affecting many biological processes in health and disease. Using whole-genome bisulfite sequencing, we report the essentially complete (92.6282%) methylome of human peripheral blood mononuclear cells (PBMC) which constitute an important source for clinical blood tests world-wide. We find the majority of CpG sites (68.4% at false positive rate of 0.46%) and only &lt;0.2% of non-CpG sites to be methylated, demonstrating that non-CpG cytosine methylation is negligible in human PBMC. Analysis of the PBMC methylome revealed a rich landscape of epigenomic data for 20 distinct features including regulatory, protein-coding, RNA gene coding, non-coding and repeat sequences. Alu element mobility, for instance, was found to negatively correlate with their methylation levels, emphasizing the critical role of DNA methylation in genome stability. Integration of our methylome data with the previously determined genome sequence of the same Asian individual analysed here, enabled a first assessment of allele-specific methylation (ASM) differences between the two haploid methylomes of any individual. Using a conservative cut-off (p &lt;0.001), we identified 599 haploid differentially methylated regions (hDMRs) covering 287 genes. Of these, 76 genes had hDMRs within 2kb of their transcriptional start sites of which &gt;80% displayed allele-specific expression (ASE) after random testing using TA clone sequencing of the same PBMC sample. These data show, that ASM is a recurrent phenomenon and highly correlated with ASE, suggesting that imprinting may be more common than previously thought. Our study not only provides a comprehensive resource for future epigenomic research but also demonstrates a paradigm of large-scale epigenomics studies through new sequencing technology. Overall design: We report the essentially complete (92.6282%) methylome of human peripheral blood mononuclear cells (PBMC) which constitute an important source for clinical blood tests world-wide.
DOI: 10.26036/cnphis0000751
title: Reduced representation library sequencing for Pacific white shrimp

description: We selected eight animals, and equal amounts of DNA (20*g in total) was pooled and submitted for complete digestion (18 hours) using the restriction endonuclease HaeIII (GG?CC) (New England Biolabs, Beverly, MA, USA). Digested genomic DNA was loaded onto a 0.9% agarose gel and fragments of sizes roughly 1-4 kb were cut and purified QIAEX II Gel Extraction Kit (Qiagen). Using a NanoDrop 1000 spectrophotometer, the final product was quantified to be 10.8 ng/*l with a total volume 50 *l. The massive parallel DNA sequencing was performed on an Illumina/Solexa Genome Analyzer II. We selected the option of single read and 75 cycles of sequencing on six lanes.
DOI: 10.26036/cnphis0000752
title: Metagenomic Analysis of the Structure and Function of the Human Gut Microbiota in Crohn''s Disease

description: This study aims to unravel the contribution of the bacteria that normally inhabit the human gastrointestinal tract to Crohn''s disease by using a multidisciplinary approach to study changes in the structure and function of gut microbial communities in three sets of patient cohorts who have Crohn''s disease. These results will be compared with those obtained from the study of healthy individuals and have the potential to identify new biomarkers of disease severity, location, and progression.
DOI: 10.26036/cnphis0000753
title: Diet, Genetic Factors, and the Gut Microbiome in Crohn''s Disease

description: The bacteria present in the intestinal tract, known as the gut microbiome, probably play a role in the pathogenesis of Crohn''s disease, but the mechanism remains unclear. In this study, we propose to determine the composition of the gut microbiome associated with Crohn''s disease while controlling for confounding factors known to alter the gut microbiome, such as host genetics and diet. These studies will provide a clearer vision of the types of bacteria associated with Crohn''s disease and provide new insights into pathogenic mechanisms and potential therapy.
DOI: 10.26036/cnphis0000754
title: Tumor Progression Revealed by Single Cell Sequencing

description: Genomic analysis provides insights into the role of copy number variation in disease, but most current methods are not designed to resolve mixed populations of cells. Methods for analysis of single cells at select loci1,2,3 are available but until recently there were no reliable methods for genome-wide assessment. The existing methods4,5,6 offer limited improvement over cytological techniques that have been available since the 1980’s. The lack is particularly acute in the analysis of genetically heterogeneous tumors, where multiple subpopulations each with distinct mutational histories co-exist7,8,9. Here we have combined whole genome amplification (WGA) and massively parallel DNA sequencing to achieve robust single cell copy number profiles with a resolution of nearly 50 kilobases in a method we call single nucleus sequencing (SNS). We apply this method first to single cells from cultures and show that there is only minor genetic variation. Then we use this technique to profile 100 single cells isolated from a basal-like breast cancer we know to be genetically heterogeneous10. We observe a few distinct subpopulations, an observation that supports a model for tumor progression in which a few sequential clonal expansions form the mass of the tumor. Moreover, we detect significant numbers of pseudodiploid cells that do not share genomic markers with the major expansions, and these cells may signify the presence of potentially large unstable diploid tumor subpopulation not revealed by previous genomic methods.
DOI: 10.26036/cnphis0000755
title: Patiria miniata genome sequencing project

description: None
DOI: 10.26036/cnphis0001447
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001448
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001449
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001450
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001451
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001452
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001454
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001455
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002135
title: Gryllotalpa major Raw sequence reads

description: Designing SSR markers from raw high-throughput reads to assess population genetic structure
DOI: 10.26036/cnphis0002136
title: RNA-seq time-course analysis of the transcriptional dynamics of the two root-infecting fungi Colletotrichum tofieldiae (mutualistic) and Colletotrichum incanum (pathogenic) and their plant host Arabidopsis thaliana during root colonization

description: The objective of this study was on the one hand to compare the transcriptional dynamics of mutualistic Colletotrichum tofieldiae and pathogenic Colletotrichum incanum during colonization of Arabidopsis roots and on the other hand also examine the corresponding host responses Overall design: Arabidopsis seeds that were either untreated (mock) or inoculated with Colletotrichum tofieldiae (isolate 0861) or Colletotrichum incanum (isolate MAFF230704) were grown in normal (P+) or low (P-) phosphate conditions. Roots (with/without fungal colonization) were collected at 6, 10, 16, and 24 days post inoculation (dpi). Additionally, C. tofieldiae and C. incanum in vitro hyphae were collected after two days growth in liquid Mathur’s medium. For each condition three replicates were obtained.
DOI: 10.26036/cnphis0002137
title: Glycine max Variation

description: In this work, we perform a detailed examination of the imputation of missing genotypes in a catalog of SNP markers obtained via a genotyping by sequencing (GBS) approach among a collection of 301 soybean lines. In addition, we extend the work by using imputation to integrate two highly complementary SNP datasets (from GBS and a SNP array). In all cases, we measured the accuracy of genotype imputation through the resequencing of a subset of the lines and show that the resulting datasets are highly accurate. In a final segment of the work, we show that performing genome-wide association scans with superior marker coverage (resulting from marker imputation) leads to improved QTL detection.
DOI: 10.26036/cnphis0002138
title: Conus tribblei Genome sequencing and assembly

description: Characterizing the structural organization and distribution of conopeptide genes in Conus genomes is important as such information will provide insights into the biology, biochemistry, and evolution of venom production in Conus species.
DOI: 10.26036/cnphis0002139
title: GenomeTrakr Project: SDSU Veterinary & Biomedical Sciences/ DOH South Dakota

description: Whole genome sequencing of cultured Salmonella enterica as part of the US Food and Drug Administration''s WGS surveillance effort for the rapid detection of foodborne illness outbreaks.
DOI: 10.26036/cnphis0002140
title: 454 sequencing project for 14 marine invertebrates

description: 454-Roche genomic libraries for 14 marine invertebrates
DOI: 10.26036/cnphis0002141
title: Kryptolebias marmoratus strain:FDS08 Genome sequencing

description: Kmar WGS
DOI: 10.26036/cnphis0002142
title: transcriptome of six different developmental stages of Rapana venosa

description: In this study, in order to obtain a more comprehensive EST database for larval development of R. venosa, we have used Illumina Hi-seq2500 platform to perform the transcriptome sequencing from 6 different developmental stage (one spiral whorl stage, two spiral whorls stage, earlier stage of three spiral whorls, later stage of three spiral whorls, four spiral whorls stage(competent larva), postlarva .This information would provide access to the genetic and genomic research on the gastropod R. venosa.
DOI: 10.14457/cu.res.2005.57
title: การศึกษาการเพิ่มความรุนแรงของแผ่นดินไหว เนื่องมาจากสภาพดิน (Site Amplification) ในบริเวณกรุงเทพมหานครและจังหวัดเชียงราย
DOI: 10.26036/cnphis0000756
title: Small RNAs in transgenic TaNAM-RNAi wheat plants

description: To explore the effect of stable RNAi on the small RNA (sRNA) population in wheat, we constructed a sRNA library from hexaploid wheat that expresses an RNAi construct under the 35S promoter that targets the endogenous NO APICAL MERISTEM (TaNAM) gene. The presence of this RNAi transgene causes a 40% reduction in expression of the target genes as measured by quantitative RT-PCR and significantly delays senescence and reduces remobilization of N, Fe, and Zn to the grain. Overall design: RNA was extracted from flag-leaves of transgenic NAM-RNAi plants at 12 days post-anthesis. RNA was collected from a pool of flag-leaves from four plants.
DOI: 10.26036/cnphis0000757
title: Solenopsis invicta genome sequencing project

description: A 454 shotgun sequencing library and an Illumina 330bp-insert paired-end library were built from the DNA of the single focal haploid male. These libraries made up 93.8% of our sequencing effort. The focal male had the Gp-9 B genotype. He was the son of a queen from a multiple-queen colony originally collected near Athens, Georgia, USA in 2008. Upon transfer of the colony to the laboratory, the queen had been isolated with workers for one year to ensure that all progeny in the colony were hers. To permit bridging of repeats that could be longer than the 454 read length, we additionally constructed 8kb and 20kb-insert paired-end 454 libraries for the remaining 6.2% of sequencing effort. The 8kb and 20kb libraries were respectively constructed from DNA pooled from ten and thirty-one brothers of the focal male, all having the Gp-9 B genotype.
DOI: 10.26036/cnphis0000758
title: Okaloosa Darter

description: High-throughput sequencing affords a cost and time effective means of obtaining large numbers of genetic markers for conservation studies. Here, we present thousands of novel microsatellite loci developed for the Okaloosa darter, Etheostoma okaloosae, an endangered percid fish. We sequenced over 29 million base pairs using 454 whole genome shotgun sequencing and employed free, user-friendly bioinformatics tools to screen for microsatellite loci and design appropriate primers. We tested 39 primer sets for polymorphism and ran population-level analyses on a population of Okaloosa darters. Of these, 30 markers were variable with an observed and expected heterozygosity of 0.382 and 0.430 respectively, and allele numbers ranging from two to 13. Comparisons against the zebrafish reference genome, Danio rerio, revealed that these loci represent an adequate chromosomal coverage of the darter genome, although total genomic coverage was only 2.4-3.3%. We also tested these loci on the brown darter, E. edwini and identified loci that will be useful for hybridization studies between these taxa.
DOI: 10.26036/cnphis0000759
title: Mosquito-associated viral metagenomics

description: Total viral DNA isolated from Culex erythrothorax mosquitoes. Culex eythrothorax was trapped by the overflow pond at San Diego Wild Animal Park.
DOI: 10.26036/cnphis0000760
title: Lepeophtheirus salmonis pacific genome sequencing project

description: The Lepeophtheirus salmonis genome was sequenced by the University of Victoria using a whole genome shotgun (WGS) approach, using genomic DNA from a single individual from Sidney, BC Canada. The estimated 600 Mb genome was sequenced to 6-8 fold coverage.
DOI: 10.26036/cnphis0000761
title: Linepithema humile genome sequencing project

description: The <i>Linepithema humile</i> genome was sequenced using 454 and Illumina sequencing technologies. Unpaired 454 sequencing reads were generated using genomic DNA from a single queen pupae, and additional paired-end 454 and Illumina sequencing reads were generated from 3kb and 8kb libraries constructed from the whole-body genomic DNA of 100 adult workers. The queens and workers were both obtained from the genetically bottlenecked California supercolony located in an orchard in Santa Clara county, California (N 37 deg. 15'' 23.5", W 122 deg. 00'' 55.2")
DOI: 10.26036/cnphis0000762
title: Asian citrus psyllid genome sequencing project

description: The <i>Diaphorina citri</i> genome has been selected for genome sequencing by the USDA. DNA will be provided by the U.S. Horticultural Research Lab. Citations: Boykin, LM, Bagnall, RA, Frohlich, DR, Hall, DG, Hunter, WB, Katsar, CS, McKenzie, CL, Rosell, RC, Shatters, Jr, RG. 2007. Twelve polymorphic microsatellite loci from the Asian citrus psyllid, Diaphorina citri Kuwayama, the vector for citrus greening disease, Huanglongbing. Molecular Ecology Notes: online (doi: 10.111/j1471-8286.2007.01831.x). Marutani-Hert, M., Hunter, WB, Katsar, CS, Sinisterra, XH., Hall, DG., Powell, CA. 2009. Reovirus-like sequences isolated from adult Asian citrus psyllid, (Hemiptera: Psyllidae: Diaphorina citri). Florida Entomologist 92:314-320. Hunter,WB, Dowd, SE, Katsar, CS, Shatters, Jr, RG, McKenzie, CL, Hall, DG. 2009. Psyllid biology: expressed genes in adult Asian citrus psyllids, Diaphorina citri Kuwayama. The Open Entomology Journal 3: 18-29. Marutani-Hert, M, Hunter, WB, Hall, DG. 2009. Establishment of Asian Citrus Psyllid (Diaphorina citri) Cell Lines. In Vitro Cellular & Developmental Biology-Animal. 45:317-320. Hunter, W.B., Bextine, B.B. 2010. Emerging psyllid genomics: Applications to reduce plant disease. Florida Scientist 73(1):3. AGR-04, Online: www.barry.edu/fas/.