cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26036/cnphis0001625
title: Database for Reference Grade Microbial Sequences (FDA-ARGOS)

description: In May 2014, the FDA and collaborators established a publicly available dAtabase for Reference Grade micrObial Sequences called FDA-ARGOS. With funding support from FDA's Office of Counterterrorism and Emerging Threats (OCET) and DoD, the FDA-ARGOS team are initially collecting and sequencing 2000 microbes that include biothreat microorganisms, common clinical pathogens and closely related species. Currently, FDA-ARGOS microbial genomes are generated in 3 phases. Generally: Phase 1 entails collection of a previously identified microbe and nucleic acid extraction. Phase 2, the microbial nucleic acids are sequenced and de novo assembled using Illumina and PacBio sequencing platforms at the Institute for Genome Sciences at the University of Maryland (UMD-IGS). Phase 3, the assembled genomes are vetted by an ID-NGS subject matter expert working group consisting of FDA personnel and collaborators and the data are deposited in NCBI databases. The FDA-ARGOS genomes meet the quality metrics for reference-grade genomes for regulatory use. FDA-ARGOS reference genomes have been de novo assembled with high depth of base coverage and placed within a pre-established phylogenetic tree. Each microbial isolate in the database is covered at a minimum of 20X over 95 percent of the assembled core genome. Furthermore, sample specific metadata, raw reads, assemblies, annotation and details of the bioinformatics pipeline are available.
DOI: 10.26036/cnphis0001626
title: Capra hircus Transcriptome or Gene expression

description: dairy goat mammary gland transcriptome information using RNA sequencing
DOI: 10.26036/cnphis0001627
title: Limulus polyphemus Genome sequencing

description: Limulus polyphemus whole genome sequencing, as part of a wider investigation of Xiphosuran genomics
DOI: 10.26036/cnphis0001628
title: Drosophila simulans strain M252 assembly

description: Assembly and annotation
DOI: 10.26036/cnphis0001629
title: European Greenfinch (Carduelis chloris) Whole blood transcriptome and Gene expression following an immune challange

description: This is the first large scale transcriptional profiling of immune function of passerine birds. The transcriptomic data generated suggest novel markers for assessment of immunological state of wild passerines.
DOI: 10.26036/cnphis0001630
title: Spiophanes tcherniai Genome sequencing

description: Most Antarctic marine invertebrates have narrow temperature tolerance ranges from -2 to +2 C. Given the predicted impact of Global warming on sea surface temperatures, we need to understand the gene structure and composition, gene regulation, and epigenetic modifications of polar organsims in response to rising sea water temperatures. The sequence data deposited here are the first pass at genome sequencing for the endemic Antarctic polychaete, Spiophanes tcherniai.
DOI: 10.26036/cnphis0001631
title: Genomic sequencing of Dactylopius coccus (Domestic cochineal) along with its Wolbachia endosymbiont Genome sequencing

description: Phylogeographic analysis of Mexican and Peruvian cochineal isolates. We also characterised the Wolbachia endosymbiont for Dactylopius coccus since Wolbachia sometimes provides phylogeographic information.
DOI: 10.26036/cnphis0001632
title: Zonotrichia leucophrys gambelii strain:Gambel''s white-crowned sparrows Transcriptome or Gene expression

description: RNA sequencing reads from Gambel''s white-crowned sparrow hypothalamus
DOI: 10.26036/cnphis0002309
title: Vigna subterranea Transcriptome or Gene expression

description: Low temperature stress in a number of African countries, such as Botswana, at night can effect the growth and development of bambara groundnut, leading to losses in potential crop yield. Therefore, we made an attempt to identify and analyze the genes and gene modules associated with low temperature stress response in bambara groundnut using the cross-species microarray technique, as bambara groundnut has no microarray chip, coupled with network-based analysis. Overall design: Two plants of the bambara groundnut genotype 'S19-3' were grown in controlled environment growth rooms at Sutton Bonington Campus, University of Nottingham under a 12 hour photoperiod and at a constant temperature of 27°C. Plants were grown in soil columns containing a growing medium of 1 part John Innes 2 compost to 1 part sand, and were watered as required. A single, fully-expanded leaflet was sampled from each of the three plants growing at 27°C, snap frozen in liquid nitrogen and stored at -80°C. Plants were given a further 3 days at 27°C to recover from sampling before being moved to a controlled environment room at 23°C. On the fifth day at 23°C a single fully-expanded leaflet was sampled and stored, as described above. After 3 further days plants were moved to 18°C, and then five days later were sampled again.
DOI: 10.26036/cnphis0002310
title: ATAC-Se1 to investigate the spatial choreography of the accessible genome

description: In order to completely understand the spatial choreography of the accessible genome in the 3D intact nucleus, we had developed a new technique termed assay of transposase accessible chromatin by visualization (ATAC-see). In brief, we had labeled the adaptor in hypersensitive Tn5 transposase with fluorophore dye and performed the Tn5 tagmentation on the fixed culture cells slide. We had performed ATAC-see in different types of cells and found out there are cell types specific spatial choreography of the accessible genome in the 3D intact nucleus, which is tightly linked to cell types specific function. Importantly, we could images the open chromatin distribution and do the sequencing on the exactly same sample, which offer a powerful tool to understand how the open chromatin organize in the 3D nucleus and how the open chromatin regulate gene expression. Overall design: We had compared the ATAC-seq libraries under different conditions such as with different Tn5s (Illumina Nextera Tn5, home-made Tn5 with and without Atto labeled on the adaptors in GM12878 cells), with and without fixation (in HT1080 cells ) and the cells growing on different materials (growing HT1080 cells on slide and suspensions cells in the tubes). In addition, we had performed ATAC-seq in human neutrophil.
DOI: 10.26036/cnphis0002311
title: Eumigus monticolus Raw sequence reads

description: Genomic comparison of a B-carrying individual with a 0B individual of Eumigus monticula with low coverage sequencing
DOI: 10.26036/cnphis0002312
title: Zea mays Genome sequencing and assembly

description: Zea mays (maize) has the highest world-wide production of all grain crops, yielding 875 million tonnes in 2012 (http://faostat.fao.org/). Although a food staple in many regions of the world, most is used for animal feed and ethanol fuel. Maize was domesticated from wild teosinte in Central America and its cultivation spread throughout the Americas by Pre-Columbian civilizations. In addition to its economic value, maize is an important model organism for studies in plant genetics, physiology, and development. It has a large genome of of about 2.4 gigabases with a haploid chromosome number of 10 (Schnable et al., 2009; Zhang et al., 2009). Maize is distinguished from other grasses in that its genome arose from an ancient tetraploidy event unique to its lineage. The maize B73 reference genome has been revised three times since its initial release as a BAC-by-BAC assembly in 2009 (Schnable et al., 2009). This entirely new assembly of the maize genome (B73 RefGen_v4) is constructed from PacBio Single Molecule Real-Time (SMRT) sequencing at approximately 60-fold coverage and scaffolded with the aid of a high-resolution whole-genome restriction (optical) mapping. The pseudomolecules of maize B73 RefGen_v4 are assembled nearly end-to-end, representing a 52-fold improvement in average contig size relative to the previous reference (B73 RefGen_v3).
DOI: 10.26036/cnphis0002313
title: Salmonella serovar Heidelberg genome sequencing

description: This study was conducted to evaluate whole-genome sequencing and phylogenetic analysis as an alternative to conventional pulsed-field gel electrophoresis subtyping for Salmonella enterica serovar Heidelberg isolates. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013 and 2014) supported by strong epidemiological evidence, as well as 13 sporadic isolates (2008-2012) were sequenced.
DOI: 10.26036/cnphis0002314
title: Panthera pardus genome sequencing and assembly

description: The leopard genome project can provide insight into evolution of big cats and their genetic characteristics.
DOI: 10.26036/cnphis0002315
title: Equus caballus Genome sequencing

description: Whole genome sequencing of Standardbred horses
DOI: 10.26036/cnphis0002316
title: A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species

description: Background: RNA-seq based on short reads generated by next generation sequencing technologies has become the main approach to study differential gene expression. Until now the main applications of this technique have been to study the variation of gene expression in a whole organism, tissue or cell type under different conditions or at different developmental stages. However, RNA-seq also has a great potential to be used in evolutionary studies to investigate gene expression divergence in closely related species. Since the more reliable statistical methods for differential gene expression inference are based on the use of raw read count data, the reference genomes of the species to be compared need to be highly comparable. Results: We show that the published genomes and annotations of the three closely related Drosophila species, D. melanogaster, D. simulans and D. mauritiana, have limitations for inter-specific gene expression studies. This is due to missing gene models in at least one of the genome annotations, unclear orthology assignments and significant length differences in the different species. We propose that published reference genomes should be re-annotated before using them as references for RNA-seq experiments to include as many genes as possible and to account for a potential length bias. For that we present a straight-forward reciprocal re-annotation pipeline that allows to reliably compare the expression for nearly all genes annotated in D. melanogaster. We carried out a RNA-seq experiment in combination with quantitative real-time PCR to confirm that the newly generated gene sets do not result in a high number of false positives as observed with references that still show a clear length difference of gene models between species. Conclusions: We conclude that our reciprocal re-annotation of previously published genomes facilitates the analysis of significantly more genes in an inter-specific differential gene expression study. We propose that the established pipeline can easily be applied to re-annotate other genomes of closely related animals and plants to improve comparative expression analyses. Overall design: mRNA profiles of larval eye-antennal imaginal discs (late L3) of three species of Drosophila (D. melanogaster OreR, D. simulans YVF and D. mauritiana TAM16) were generated by deep sequencing using Illumina HiSeq 2000. 3 biological replicates were generated for D. melanogaster sample and sequenced in 50 bp single-end reads; 3 biological replicates were generated for D. simulans sample and sequenced in 100 bp paired-end reads; 6 biological replicates were generated for D. mauritiana sample, 3 of these were sequenced in 50 bp single-end reads and the other 3 in 100 bp paired-end reads.
DOI: 10.26036/cnphis0002317
title: Holacanthus clarionensis Genome sequencing

description: Samples of Holacanthus clarionensis (voucher no. 228) were purchased from local aquarium and originally imported from Mexico. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0001633
title: Aegypius monachus Genome sequencing

description: PGI, National Museum of Korea, and collaborators are working on the Cinereous Vulture whole genome sequencing and analysis.
DOI: 10.26036/cnphis0001634
title: Provanna sp. JWQ-2014 Genome survey sequencing

description: Mitochondrial assembly
DOI: 10.26036/cnphis0001635
title: Expression data from proximal, middle, and distal segments of E6.5 chicken cochlea

description: Precise frequency discrimination is a hallmark of auditory function in birds and mammals. In the cochlea, tuning and spectral separation result from longitudinal differences in basilar membrane stiffness and numerous individual gradiations in sensory hair cell phenotypes, but it is unknown what patterns those phenotypes. Hypothesizing that morphogen levels might differ along the longitudinal axis of the developing cochlea, we sequenced the transcriptomes of the proximal, middle, and distal thirds of the chicken cochlea at E6.5, when postmitotic hair cells first form. Overall design: Embryonic day 6.5 chicken cochlea were dissected. Three samples were collected from each cochlear duct by cutting the duct into three approximately equal sized pieces to produce proximal, middle, and distal pieces. Each sample contained a portion of the future tegmentum vasculosum and the basilar papilla sensory epithelium. The distal piece also contained the region fo the future lagena.
DOI: 10.26036/cnphis0001636
title: Hybridization capture using short PCR products enriches small genomes by Capturing Flanking sequences (CapFlank)

description: Rodent mtDNA capture in different initial DNA concentrations Genome sequencing
DOI: 10.26036/cnphis0001637
title: Anopheles bwambae SNP

description: None
DOI: 10.26036/cnphis0001638
title: Paragonimus kellicotti Genome sequencing

description: Paragonimus spp., the lung flukes, represents one of the most injurious of the food-borne helminths. These flukes cause paragonimiasis in people and other crab-eating mammals in Asia, parts of West Africa, and South and Central America. About 20 million people are infected with lung flukes and an estimated 293 million people are at-risk (Keiser and Utzinger 2009).
DOI: 10.26036/cnphis0001639
title: Horse MeDIP-seq

description: we report the data and analyses of genome-wide DNA methylation patterns in the skeletal muscle, heart, lung, and cerebrum of TH and JH, and tissue-specific DNA methylation differences between the two horse breeds produced by methyl-DNA immunoprecipitation sequencing (MeDIP-seq).
DOI: 10.26036/cnphis0001640
title: Transcriptome sequencing of a large human family identifies the impact of rare non-coding variants

description: We have combined high-quality genome sequencing and RNA-sequencing data within a 17-individual, three generation family. Using these data, we have contrasted cis-acting expression, allele-specific expression and splicing quantitative trait loci (collectively termed eQTLs) within the family to eQTLs discovered within a cell-type and ethnicity-matched population sample. We identified that eQTL that exhibit larger effects in the family compared to the population are enriched for rare regulatory and splicing variants and were more likely to influence essential genes. In addition, we identify several large effect-size eQTLs within the family for genes involved in complex disease. Through analysis of eQTLs in a large family we also report the utility of non-coding genome annotation to predicting the effect of rare non-coding variants. We find that a combination of distance to the transcription start site, evolutionary constraint and epigenetic annotation is considerably more informative for predicting the consequence of rare non-coding variants than for common variants. In summary, through transcriptome analyses within a large family we are able to identify the contribution of rare non-coding variants to expression phenotypes and further demonstrate the predictive potential of diverse non-coding genome annotation for interpretation of the impact of rare non-coding variants. Overall design: RNA-Sequencing of CEPH/UTAH family 1463
DOI: 10.26036/cnphis0001641
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0002319
title: Pygoplites diacanthus Genome sequencing

description: Samples of Pygoplites diacanthus (voucher no. 231) were purchased from local aquarium and originally imported from Indonesia (Pacific color morph). Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002320
title: Chaetodontoplus conspicillatus Genome sequencing

description: Samples of Chaetodontoplus conspicillatus (voucher no. 232) were purchased from local aquarium and originally imported from Queensland, Australia. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002321
title: Pomacanthus xanthometopon Genome sequencing

description: Samples of Pomacanthus xanthometapon (voucher no. 236) were purchased from local aquarium and originally imported from Maldives. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002322
title: Pomacanthus imperator Genome sequencing

description: Samples of Pomacanthus imperator (voucher no. 237) were purchased from local aquarium and originally imported from Maldives. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002323
title: Chaetodontoplus mesoleucus Genome sequencing

description: Samples of Chaetodontoplus mesoleucus (voucher no. 249) were purchased from local aquarium and originally imported from Cebu, Philippines. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002324
title: Apolemichthys armitagei Genome sequencing

description: Samples of Apolemichthys armitagei (voucher no. 271) were purchased from local aquarium and originally imported from Maldives. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002325
title: Apolemichthys griffisi genome sequencing

description: Samples of Apolemichthys griffisi (voucher no. 272) were purchased from local aquarium and originally imported from Kiribati. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002327
title: Holacanthus passer Genome sequencing

description: Samples of Holacanthus passer (voucher no. 274) were purchased from local aquarium and originally imported from La Paz, Mexico. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0001642
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001643
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001644
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001645
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001646
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001647
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001648
title: Foodborne Pathgen Survey

description: Genome sequencing project
DOI: 10.26036/cnphis0001649
title: Cyprinodon variegatus isolate:N-32 Genome sequencing

description: Sheepshead minnow has been widely used to identify the effects of environmental exposure on gene expression patterns and gene regulatory activities in response to environmental stimuli. Broadening the genetic research base available to researchers working at the junction of environmental toxicology and biomedical research is likely to lead to novel insights into both short and long term effects of environmental exposure on vertebrate species.
DOI: 10.26036/cnphis0002326
title: Apolemichthys arcuatus Genome sequencing

description: Samples of Apolemichthys arcuatus (voucher no. 273) were purchased from local aquarium. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002328
title: Holacanthus africanus Genome sequencing

description: Samples of Holacanthus africanus (voucher no. 275) were purchased from local aquarium and originally imported from Ghana. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002329
title: Single Cell RNA-seq Study of Midbrain and Dopaminergic Neuron Development in Mouse, Human, and Stem Cells

description: In order to get a better molecular understanding of human midbrain development, this study defines cell types of the ventral midbrain in both human and mouse as well as stem cell-derived dopaminergic neuron preparations, and reveals the temporal dynamics of key lineages across development and the adult. Overall design: Single cells according to Samples list consisting of: Human embryo ventral midbrain cells between 6 and 11 weeks of gestation, mouse ventral midbrain cells at six developmental stages between E11.5 to E18.5, Th+ neurons at P19-P27, and putative dopaminergic neurons at P28-P56 FACS-sorted from Slc6a3-Cre/tdTomato mice. Stem cells (iPSCs and ESCs) preparation at different stages of differentiation towards Th+ neurons.
DOI: 10.26036/cnphis0002330
title: Holacanthus tricolor genome sequencing

description: Samples of Holacanthus tricolor (voucher no. 277) were purchased from local aquarium and originally imported from Miami. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).
DOI: 10.26036/cnphis0002331
title: Centropyge multicolor Genome sequencing

description: Samples of Centropyge multicolor (voucher no. 278) were purchased from local aquarium and originally imported from Marshalls Island. Total genomic DNA was extracted from muscle tissue. Paired-end genomic library was constructed by using Illumina TruSeq DNA PCR-Free Library Preparation Kits and then performed next generation sequencing by Miseq splatform (2X300bp).