cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0002102
title: Camelops hesternus Genome sequencing

description: Paleogenomic sequencing of Camelops individuals, ~130,000 years old.
DOI: 10.26036/cnphis0002103
title: Enteromyxum leei isolate:2.6.2011 Genome sequencing and assembly

description: Genome contigs of the Myxozoa Sphaeromyxa zaharoni for phylogenetic and genomic analysis. The data is contaminated with host (Sparus aurata L.) DNA.
DOI: 10.26036/cnphis0002104
title: Ancylostoma ceylanicum Genome Sequencing

description: The Genome Institute and collaborators are sequencing the hookworm, Anclyostoma ceylanicum. Hookworm diseases are extremely common in the tropics and sub-tropics, with a disease burden comparable to measles and exceeding that of diabetes and lung cancer. A. ceylanicum is a parasite that attaches to the intestine of animals - particularly hamsters - causing anemia in the host. It is a good model for studying human hookworms.
DOI: 10.26036/cnphis0002105
title: Transcriptome profiles and comparison of Arabidopsis thaliana woody (soc1-ful) and WT (Col-0) stems.

description: The douple mutant Arabidopsis thaliana soc1 ful, in contrast with WT, produces an interfascicular cambium and a large wood cylinder is the flowering stem. We present the RNAseq data for polyA mRNA of different developmental stages of cambium and wood formation in Arabidopsis thaliana. We sequenced 7 stages; 4 in the woody mutant soc1-6 ful-7 (herbaceous, cambium initiation, wood initiation and leaf) and 3 stages in the WT Col-0 (herbaceous, cambium and leaf). The corresponding stem anatomy is also presented in the manuscript indicating the stage of cambium development and the production of secondary xylem. Overall design: Sequencing of 7 differents stem developmental stage and leaf using 3 biological replicates.
DOI: 10.26036/cnphis0002106
title: Ancylostoma duodenale Genome Sequencing

description: None
DOI: 10.26036/cnphis0000719
title: Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing.

description: Sadia Bekal, Craig, J., Hudson, M., Niblack, T., Domier, L., Lambert, K. N. Abstract Heterodera glycines, the soybean cyst nematode (SCN), is a damaging agricultural pest that could be effectively managed if critical phenotypes, such as virulence and host range could be understood. While SCN is amenable to genetic analysis, lack of DNA sequence data prevents the use of such methods to study this pathogen. Fortunately, new methods of DNA sequencing that produced large amounts of data and permit whole genome comparative analyses have become available. In this study, 400 million bases of genomic DNA sequence were collected from two inbred biotypes of SCN using micro-bead DNA sequencing. Comparisons to a BAC, sequenced by Sanger sequencing, showed that the micro-bead sequences could identified low and high copy number regions within the BAC. Potential single nucleotide polymorphisms (SNPs) between the two SCN biotypes were identified by comparing the two sets of sequences. Selected resequencing revealed that up to 84% of the SNPs were correct. We conclude that the quality of the micro-bead sequence data was sufficient for SNP identification and should be applicable to organisms with similar genome sizes and complexities. The SNPs identified will be an important starting point in associating phenotypes with specific regions of the SCN genome.
DOI: 10.26036/cnphis0000720
title: Callorhinchus milii (elephant shark) genome sequencing project

description: 19.25X coverage of the 0.91 Gb genome of the elephant shark. The genomic DNA came from the testis of an individual collected near Hobart, Tasmania.
DOI: 10.26036/cnphis0000721
title: Acanthocheilonema viteae

description: None
DOI: 10.26036/cnphis0000722
title: Latimeria chalumnae strain:Wild caught Genome sequencing and assembly

description: None
DOI: 10.26036/cnphis0000723
title: Leptonychotes weddellii genome sequencing

description: Leptonychotes weddellii (Weddell Seal) genome sequencing using Illumina sequencing with multiple library types.
DOI: 10.26036/cnphis0000724
title: Anopheles gambiae Pimperena S-Form Sequencing

description: This sequencing was carried out to compare methodologies for de novo assembly of Anopheles mosquito genomes from Illumina reads. A single individual mosquito, from the An. gambiae Pimperena S colony (molecular form S), was used to generate small-insert (180 bp, 3 kb) libraries. A pool of individuals from the same colony was used to generate a library with fosmid-scale (38 kb) inserts. Reads were assembled using the ALLPATHS LG program.
DOI: 10.26036/cnphis0000725
title: Genome of cancer research specialist Kim Seong-jin

description: The study of the Korean genome sequence map is a mandatory step toward building a standard Korean genome. Using cancer research specialist Kim Seong-jin''s personal genome, researchers have completed a full genome sequence map. It is the world''s fourth identified personal genome sequence map. Since it is a personal genome sequence map, the next step is to build a standard genome for Koreans. The standard Korean genome will be able to help experts conduct personalized medical treatments based on the analyses of the individual genome
DOI: 10.26036/cnphis0000726
title: Staphylococcus aureus comparative genomics project

description: Comparative of multiple Staphylococcus aureus strains using 454 sequencing.
DOI: 10.26036/cnphis0000727
title: whole genome sequencing of the Varroa destructor genome

description: The USDA-ARS is determining the genome sequence of <i>Varroa destructor</i> using a whole genome shotgun approach. The DNA source is 2000 mites collected from colony 45 in the ''Mushroom'' apiary of the USDA-ARS Bee Research Laboratory, Beltsville, MD, USA (N39°2.49096, W076°51.83742) in September, 2008.
DOI: 10.26036/cnphis0001420
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001421
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001422
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001423
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001424
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001425
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001426
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001427
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001428
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002107
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0002108
title: Whole genome sequence of Eulemur flavifrons and Eulemur macaco

description: Our lab has used next-generation sequencing technology to produce high coverage genome-wide sequence data for a single Eulemur flavifrons individual and a single Eulemur macaco individual, in order to address questions related to the demographic history of the two species, as well as to identify candidate regions that may influence their divergent pigmentation phenotypes.
DOI: 10.26036/cnphis0002109
title: Sericostoma personatum Raw sequence reads

description: 454-Roche shallow sequencing of a genomic library of the caddisfly Sericostoma personatum
DOI: 10.26036/cnphis0002110
title: Diachasma alloeum isolate:Michigan Genome sequencing and assembly

description: The genome of Diachasma alloeum, a braconid parasitoid wasp of Rhagoletis pomonella, will be useful to answer important evolutionary questions.
DOI: 10.26036/cnphis0002111
title: Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex-biased expression and selection signals

description: The investigation of genomic variation in populations helps in understanding recent adaptive processes of ecologically relevant trait variation. The blue tit – a long time ecological model – has been used to investigate fitness consequences of different behavioural and mating strategies. However, very little is known about the underlying genetic changes due to natural and sexual selection in the genome of the bird. As a step to bridge this gap we assembled the first draft genome of a single blue tit, mapped the transcriptome of five females and five males on this reference and identified genomic variants.In the gonads we found a similar proportion of sex-limited genes within the high number of male- and female-biased genes, respectively, whereas in the brain most female-biased genes were also female-limited and most male-biased genes were located on the Z-chromosome with expression in both sexes. This indicates incomplete dosage compensation for the male-biased genes, but a different qualitative control mechanism for the female-biased genes. We called more than 500,000 SNPs from the RNA-seq data with a high specificity and sensitivity in comparison to the DNA-seq calling (both &gt; 80%). After utilizing different information of these polymorphisms we identified the strongest selection signals in the genome.We list candidate genes which can be used for further sequencing and detailed selection studies, including genes potentially related to meiotic drive evolution.
DOI: 10.26036/cnphis0002112
title: Anguilla rostrata isolate:LakeOntario-01-2011 Genome sequencing and assembly

description: American Eel genome project
DOI: 10.26036/cnphis0002113
title: Identification and profiling of microRNAs associated with white and black plumage pigmentation in the white and black feather bulbs of ducks by RNA-Sequencing

description: Purpose: MicroRNAs (miRNAs) play important roles in many biological processes by regulating gene expression at the post-transcriptional level. However, the mechanism by which specific miRNAs may regulate plumage pigmentation has remained largely elusive. In this study, we sequenced miRNAs using Solexa sequencing and then performed a detailed analysis of their expression profiles between the black and white feather bulbs of ducks. This study provides the foundation for subsequent studies on the prospective practical role for such miRNAs in post-transcriptional gene regulation linked to plumage pigmentation. Overall design: Methods: Black and white feather bulbs profiles of four ducks namely, Cui Hei, Kaiya, Liancheng pure breeds and Kaiya-Liancheng F2, were generated by illumina solexa sequencing . Three feather bulbs from the same individual duck were pooled as one samples. Samples from the same breed were pooled as one and sent to Beijing Genomics Institute (BGI, China) for small RNA library construction and sequencing. The libraries were prepared with NEBNext® UltraTM RNA Library Prep Kit. Sequencing was performed using Illumina sequencing technology (Illumina HiSeq 2000). The sequence quality was assessed with FastQC software . Clean sequence reads were analysed by miRDeep2 software version 2.1.2 . We compared the miRNA expression profiles between black and white feather libraries of ducks using the DEGseq software and our own perl script. miRNAs that adhered to the criteria log2-fold change =1 or = -1 and p-value =0.05 were considered to be differentially expressed. The Student''s t-test was used to compute the value. Validation of 10 conserved miRNAs sequencing data was performed using the SYBR Green assay.
DOI: 10.26036/cnphis0002114
title: Nannospalax galili Genome sequencing

description: These are the DNA sequences generated in a requencing study about the sympatric speciation of Spalax galili (Nannospalax galili). The details of the analysis can be found in the publication associated with this data.
DOI: 10.26036/cnphis0002115
title: Rhodeus uyekii(Korean rose bitterling)

description: Rhodeus uyekii Transcriptome or Gene expression
DOI: 10.26036/cnphis0000728
title: Onchocerca volvulus genome sequencing project

description: <b><i>Onchocerca volvulus</i> NA</b>. Light sequence coverage to characterize polymorphisms will be generated through a collaborative effort between the Broad Institute and Harvard University.
DOI: 10.26036/cnphis0000729
title: Wuchereria bancrofti Genome sequencing

description: This sequencing project will generate light sequence coverage to characterize polymorphisms from <i>Wuchereria bancrofti</i>.
DOI: 10.26036/cnphis0000730
title: Genome sequencing of Otolemur garnettii

description: The <i>Otolemur garnettii</i> genome was sequenced by the Broad Institute.
DOI: 10.26036/cnphis0000731
title: Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in T. aestivum and B. distachyon

description: The small RNA transcriptomes of bread wheat (Triticum aestivum L.) and its emerging model (Brachypodium distachyon (L.) Beauv) were obtained by using deep sequencing technology. Small RNA compositions were analyzed in these two species. In addition to 70 conserved microRNAs (miRNA) from 25 families, 23 novel wheat miRNAs were identified. For Brachypodium, 12 putative miRNAs were predicted from a limited number of ESTs, of which one was a potential novel miRNA. Also, 94 conserved miRNAs from 28 families were identified in this species. Expression validation was performed for several novel wheat miRNAs. RNA ligase-mediated 5' RACE experiments demonstrated their capability to cleave predicted target genes including three disease resistant gene analogs. Differential expression of miRNAs was observed between Brachypodium vegetative and reproductive tissues, suggesting their different roles at the two growth stages. Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in Brachypodium distachyon. Keywords: Small RNA Overall design: One wheat small RNA library (Tae) and two Brachypodium small RNA libraries (BdR and BdV) were sequenced.
DOI: 10.26036/cnphis0000732
title: UCSD Human Reference Epigenome Mapping Project

description: The human embryonic stem cells (hESCs) are a unique model system for investigating the mechanisms of human development due to their ability to replicate indefinitely while retaining the capacity to differentiate into a host of functionally distinct cell types. In addition, these cells could be potentially used as therapeutic agents in regenerative medicine. Differentiation of hESCs involves selective activation or silencing of genes, a process controlled in part by the epigenetic state of the cell. In order to gain a better understanding of the epigenetic mechanisms regulating differentiation of hESCs, and produce general reference epigenome maps of the human cells, we propose to establish an Epigenome Center in San Diego. Our center will be focused on both undifferentiated hESC and four hESC-derived early embryonic cell lineages including extraembryonic endoderm, trophoblast, mesendoderm (a common precursor to mesodermal and endodermal lineages), and mesenchymal cells (a specific mesoderm derivative). We have developed and validated high throughput technologies for mapping the state of DNA methylation and chromatin modifications throughout the genome, and will use these methods to generate high-resolution maps of the reference epigenomes. Specifically, we will grow and differentiate hESCs into multiple lineages, and map DNA methylation sites using a newly developed technology that combines bisulfite conversion and whole genome shotgun sequencing. We will also determine the histone modification status in the genome by performing both ChlP-chip and ChlP-Seq analysis. We will develop advanced statistical and algorithmic solutions to facilitate high-throughput sequencing data analysis, and establish an informatics pipeline for collecting, storage, and distribution of epigenome maps. Finally, we will perform integrated data analysis to identify new epigenetic patterns in the genome that could provide insights in mechanisms of epigenetic regulation.
DOI: 10.26036/cnphis0000734
title: BI Human Reference Epigenome Mapping Project

description: The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. Characterization of the reference epigenome in humans by use of ChIP-Seq in a diverse panel of ES cells, tissue stem cells, reprogrammed stem cells, primary cells and tissues.
DOI: 10.26036/cnphis0000735
title: The stickleback genome sequencing project

description: A first draft of the three spine stickleback fish genome is available.
DOI: 10.26036/cnphis0000736
title: Pleurobrachia bachei Genome sequencing and assembly

description: Sequence the genome of the first Ctenophore.
DOI: 10.26036/cnphis0000737
title: Phaseolus vulgaris cultivar:G19833 Genome sequencing and assembly

description: <i>Phaseolus vulgaris</i> genome WGS sequencing project from JGI.
DOI: 10.26036/cnphis0001429
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001430
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001431
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001432
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001433
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001434
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001435
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001436
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0001437
title: Foodborne Pathogen Survey

description: Genome Sequencing Project
DOI: 10.26036/cnphis0002116
title: Octopus bimaculoides Transcriptome or Gene expression

description: Transcriptome sequencing of Octopus bimaculoides
DOI: 10.26036/cnphis0002117
title: Gentiana straminea Transcriptome or Gene expression

description: functional research on natural product biosynthesis
DOI: 10.26036/cnphis0002118
title: Brassica juncea var. timuda genome sequencing and assembly

description: The Brassica family possesses includes many economically relevant species that are important for human nutrition worldwide.The Brassica genus contains a diverse range of oilseed and vegetable crops contributing that are important for much to human nutrition. B. juncea was formed by polyploidization between the diploid ancestors of B. rapa and B. nigra, followed by spontaneous chromosome doubling. Subsequent diversifying selection mainly then gave rise mainly to the vegetable and oilseed sub-variety subvarieties in B. juncea.
DOI: 10.26036/cnphis0002119
title: Aedes aegypti strain:Moyo-S and Moyo-R Variation

description: NextGen sequencing (Hiseq) of Moyo-S and Moyo-R strains of Aedes aegypti. The sequences are generated to identify genetic variations between the two strains.
DOI: 10.26036/cnphis0002120
title: GenomeTrakr Project: Texas Department of State Health Services

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/cnphis0002121
title: NOVEL ADOPTIVE IMMUNOTHERAPY APPROACH THROUGH MIHA TARGETING

description: Personalized anti-cancer treatment based on our proprietary geno-proteomic approach that hinges on a combination of next generation sequencing and high-throughput mass spectrometry (MS) peptide identification.
DOI: 10.26036/cnphis0002122
title: Asymmetron lucayanum isolate:AD20110701 Genome sequencing

description: WGS sequencing
DOI: 10.26036/cnphis0002123
title: Mesodinium Rubrum strain:MR-MAL-01 Transcriptome or Gene expression

description: Transcriptomic analysis of Mesodinium rubrum
DOI: 10.26036/cnphis0002124
title: Teleaulax amphioxeia strain:CR-MAL 01 Transcriptome or Gene expression

description: Transcriptomic analysis of Teleaulax amphioxeia
DOI: 10.26036/cnphis0000738
title: From raw materials to validated system: The construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite

description: Manuscript accepted pending revisions in Physiological Genomics. The limited availability of genomic tools and data for non-model species impedes computational and systems biology approaches in non-model organisms. Here we describe the development, functional annotation, and utilization of genomic tools for the avian wildlife species Northern bobwhite (Colinus virginianus) to determine the molecular impacts of exposure to 2,6-dinitrotoluene (2,6-DNT), a field-contaminant of military concern. Massively-parallel pyrosequencing of a normalized multi-tissue library of Northern bobwhite cDNAs yielded 71,384 unique transcripts which were annotated using gene ontology (GO), pathway information and protein domain analysis. Comparative genome analyses with model organisms revealed functional homologies in 8,825 unique Northern bobwhite genes that are orthologous to 48% of Gallus gallus protein-coding genes. Pathway analysis and GO enrichment of genes differentially expressed in livers of birds exposed for 60d to 10 and 60 mg/kg/d 2,6-DNT revealed several impacts validated by RT-qPCR including: prostaglandin pathway-mediated inflammation, increased expression of a heme synthesis pathway in response to anemia and a shift in energy metabolism toward protein catabolism via inhibition of control points for glucose and lipid metabolic pathways, PCK1 and PPARGC1, respectively. This research effort provides the first comprehensive annotated gene library for Northern bobwhite. Transcriptome analysis provided insights into the metabolic perturbations underlying several observed toxicological phenotypes in a 2,6-DNT-exposure case study. Further, the systemic impact of dinitrotoluenes on liver function appears conserved across species as PPAR signaling is similarly affected in fathead minnow liver tissue after exposure to 2,4-DNT.
DOI: 10.26036/cnphis0000739
title: BI Human Reference Epigenome Mapping Project: ChIP-Seq in human subject

description: Characterization of the reference epigenome in humans by use of ChIP-Seq in a diverse panel of ES cells, tissue stem cells, reprogrammed stem cells, primary cells and tissues.
DOI: 10.26036/cnphis0000740
title: Pongo pygmaeus Genome sequencing

description: None