cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100493
title: Supporting data for "Sequana Coverage: Detection and Characterization of Genomic Variations using Running Median and Mixture Models."

description: In addition to mapping quality information, the Genome coverage contains valuable biological information like the presence of repetitive regions, deleted genes or copy number variations. It is essential to take into consideration atypical regions, trends (e.g., origin of replication) or known and unknown biases that influence coverage. It is also important that reported events have robust statistics (e.g. z-score) associated with their detections as well as precise location. <br>We provide a standalone application sequana_coverage that reports genomic regions of interest (ROIs) which are significantly over- or under-represented in HTS sequencing data. Significance is associated with the events as well as characteristics such as length of the regions. The algorithm first detrends the data using an efficient running median algorithm. It then estimates the distribution of the normalized genome coverage with a Gaussian mixture model. Finally, a z-score statistic is assigned to each base position and used to separate the central distribution from the ROIs (i.e., under- and over-covered regions). A double thresholds mechanism is used to cluster the genomic ROIs. HTML reports provide a summary with interactive visual representations of the genomic ROIs with standard plots and metrics. Genomic variations such as single nucleotide variants (SNVs) or copy number variations (CNVs) can be effectively identified at the same time.
DOI: 10.5524/100501
title: Supporting data for "PiGx: Reproducible genomics analysis pipelines with GNU Guix"

description: In bioinformatics, as well as other computationally-intensive research fields, there is a need for workflows that can reliably produce consistent output, from known sources, independent of the software environment or configuration settings of the machine on which they are executed. Indeed, this is essential for controlled comparison between different observations or for the wider dissemination of workflows. Providing this type of reproducibility and traceability, however, is often complicated by the need to accommodate the myriad dependencies included in a larger body of software, each of which generally come in various versions. Moreover, in many fields (bioinformatics being a prime example), these versions are subject to continual change due to rapidly evolving technologies, further complicating problems related to reproducibility. Here, we propose a principled approach for building analysis pipelines and managing their dependencies. As a case study to demonstrate the utility of our approach, we present a set of highly reproducible pipelines for the analysis of RNA-seq, ChIP-seq, Bisulfite-seq, and single-cell RNA-seq. All pipelines process raw experimental data, and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables. Users may install these highly reproducible packages and apply them to their own datasets without any special computational expertise beyond the use of the command line. We hope such a toolkit will provide immediate benefit to laboratory workers wishing to process their own data sets or bioinformaticians seeking to automate all, or parts of, their analyses. In the long term, we hope our approach to reproducibility will serve as a blueprint for reproducible workflows in other areas. Our pipelines, along with their corresponding documentation and sample reports, are available at http://bioinformatics.mdc-berlin.de/pigx
DOI: 10.5524/100503
title: Supporting data for "The genome of common long-arm octopus Octopus minor"

description: The common long-arm octopus (<i>Octopus minor</i>) is found in mudflats of subtidal zones and faces numerous environmental challenges. The ability to adapt its morphology and behavioural repertoire to diverse environmental conditions makes the species a promising model to understand genomic adaptation and evolution in cephalopods.<br>The final genome assembly of <i>O. minor</i> is 5.09 Gb, with a contig N50 size of 197 kb and longest size of 3.027 Mb, from a total of 419 Gb raw reads generated using PacBio RS II platform. We identified 30,010 genes and 44.43% of the genome is composed of repeat elements. The genome-widw phylogenetic tree indicated the divergence time between <i>O. minor</i> and <i>O. bimaculoides</i> was estimated to be 43 million years ago (Mya) based on single-copy orthologous genes. In total, 178 gene families are expanded in <i>O. minor</i> in the bilaterian species. <br> We found that the <i>O. minor</i> genome was larger than that of closely related <i>O. bimaculoides</i>, and this difference could be explained by enlarged introns and recently diversified transposable elements. The high-quality <i>O. minor</i> genome assembly provides a valuable resource for understanding octopus genome evolution and the molecular basis of adaptations to mudflats.
DOI: 10.5524/100504
title: Supporting data for "The draft genomes of five agriculturally important African orphan crops"

description: A continued growth in the world population is expected to double the worldwide demand for food by 2050. Moreover, 88% of countries are currently facing a serious burden of malnutrition, especially in Africa and Southern & South-Eastern Asia. 30 species alone contribute 95% of the present food energy needs of humans with wheat, maize and rice providing the majority of calories. Therefore, to diversify and stabilize global food supply, enhance agricultural productivity and tackle malnutrition in these countries, a greater utilization of neglected or underused crops (orphan crops) could be a partial solution. Here we present draft genome information from five agriculturally, biologically, medicinally and economically important African orphan crops, namely; <em>Vigna subterranea</em>, <em>Lablab purpureus</em>, <em>Faidherbia albida</em>, <em>Sclerocarya birrea</em>, and <em>Moringa oleifera</em>. The assembled genomes range in size from 217 to 654 Mb. In addition, we have predicted 31707, 20946, 28979, 18937, 18451 protein-coding genes in <em>V. subterranea</em>, <em>L. purpureus</em>, <em>F. albida</em>, <em>S. birrea</em> and <em>M. oleifera</em> respectively. We have further analyzed the expansion and contraction of selected gene families, and characterized root-nodule-symbiosis genes, transcription factors and starch biosynthesis related genes in these genomes. This genome data will be useful to identify and characterize agronomically important genes and understand their mode of actions, enabling genomics-based, evolutionary studies, and breeding strategies for designing faster, focused and predictable crop improvement programs.
DOI: 10.5524/100507
title: Supporting data for "A network-based conditional genetic association analysis of the human metabolome"

description: Genome-wide association studies have identified hundreds of loci that influence a wide variety of complex human traits; however, little is known regarding the biological mechanism of action of these loci. The recent accumulation of functional genomics (omics), including metabolomics data, has created new opportunities for studying the functional role of specific changes in the genome. Functional genomic data are characterized by their high dimensionality, the presence of (strong) statistical dependency between traits, andpotentiallycomplex genetic control. Therefore, the analysis of such data requires specific statistical genetics methods. To facilitate our understanding of the genetic control of omics phenotypes, we propose a trait-centered, network-based conditional genetic association (cGAS) approach for identifying the direct effects of genetic variants on omics-based traits. For each trait of interest, we selected from a biological network a set of other traits to be used as covariates in the cGAS. The network can be reconstructed either from biological pathway databases (a mechanistic approach) or directly from the data, using a Gaussian Graphical Model applied to the metabolome (a data-driven approach). We derived mathematical expressions which allow comparison of the power of univariate analyses with conditional genetic association analyses. We then tested our approach using data from a population-based KORA study (n=1784 subjects, 1.7 million SNPs) with measured data for 151 metabolites. We found that compared to single-trait analysis, performing a genetic association analysis that includes biologically relevant covariates can either gain or lose power, depending on specific pleiotropic scenarios, for which we provide empirical examples. In the context of analyzed metabolomics data, the mechanistic network approach had more power compared to the data-driven approach. Nevertheless, we believe that our analysis shows that neither a prior-knowledge-only approach nor a phenotypic-data-only approach is optimal, and we discuss possibilities for improvement.
DOI: 10.5524/100510
title: Supporting Data for "Activity changes in neuron-astrocyte networks in culture under the effect of norepinephrine"

description: Monitoring the activity and morphology of Neuron-astrocyte networks in culture is powerful tool for studying dynamics, structure and communication in neuron-astrocyte networks independently or as a model of sub-brain network. These cultures are known to produce stereotypical patterns of activity e.g. highly synchronized network burst resembling sleep or seizure states, thus it enables to explore behaviors that can relate to brain function and disease. High-resolution microscopy of calcium imaging combined with simultaneous electrical recording provides a comprehensive overview on the networks dynamics. This set-up enables to apply global perturbations of electrical and chemical stimulation on the cultures during the recording task, and record the effects on network activity on line. Morphological changes in the cultures can be obtained to have a complete dataset for structure-function study of neuron-astrocyte networks in vitro.<br>The 4TB of data presented here was recorded and imaged as part of an accompanying study looking at in vitro structure-function of neuron-astrocyte networks. Simultaneous optical (calcium imaging) and electrical (MEA) recordings lasted 5-12 minutes and included spontaneous activity recording, electrical and chemical stimulation of neuron-astrocyte and isolated astrocyte cultures. Production procedures, experimental protocols and reuse options are included. The data has been suitable to reveal changes in the activity and morphology of the cultures and enabled observation and analysis of neuron-astrocyte and isolated astrocyte cultures behaviors under the applied perturbations.<br>Our dataset is sufficient to show significant changes in activity and morphology of neuron-astrocytes networks in culture under the applied stimulations. Over 100 recordings of 58 different cultures gives insight of the observations significance and led to conclusions about astrocyte activity and neuron-astrocyte network communication. Making it available here will allow others to test new tools for calcium imaging analysis and extracellular neuronal voltage recordings.
DOI: 10.5524/100483
title: Supporting data for "Draft genome assembly of the invasive cane toad, <i>Rhinella marina</i>"

description: The cane toad (<i>Rhinella marina</i> formerly <i>Bufo marinus</i>) is a species native to Central and South America that has spread across many regions of the globe. Cane toads are known for their rapid adaptation and deleterious impacts on native fauna in invaded regions. However, despite an iconic status, there are major gaps in our understanding of cane toad genetics. The availability of a genome would help to close these gaps and accelerate cane toad research. <br> We report a draft genome assembly for <i>R. marina</i>, the first of its kind for the Bufonidae family. We used a combination of long read PacBio RS II and short read Illumina HiSeq X sequencing to generate a total of 359.5 Gb of raw sequence data. The final hybrid assembly of 31,392 scaffolds was 2.55 Gb in length with a scaffold N50 of 168 kb. BUSCO analysis revealed that the assembly included full length or partial fragments of 90.6% of tetrapod universal single-copy orthologs (n=3950), illustrating that the gene-containing regions have been well-assembled. Annotation predicted 25,846 protein coding genes with similarity to known proteins in SwissProt. Repeat sequences were estimated to account for 63.9% of the assembly. <br>The <i>R. marina</i> draft genome assembly will be an invaluable resource that can be used to further probe the biology of this invasive species. Future analysis of the genome will provide insights into cane toad evolution and enrich our understanding of their interplay with the ecosystem at large.
DOI: 10.5524/100492
title: Supporting data for "Extensive evaluation of the generalized relevance network approach to inferring gene regulatory networks"

description: The generalized relevance network approach to network inference reconstructs network links based on the strength of associations between data in individual network nodes. It can reconstruct undirected networks, i.e. relevance networks, sensu stricto approach, as well as directed networks, approach referred to as causal relevance networks. The generalized approach allows the use of an arbitrary measure of pairwise association between nodes, an arbitrary scoring scheme that transforms the associations into weights of the network links, and a method for inferring the directions of the network links. While this makes the generalized relevance network approach powerful and flexible, it introduces the challenge of finding a combination of components that would perform well on a given inference task. We address this challenge by performing an extensive empirical analysis of the performance of 114 variants of the generalized relevance network approach on 47 tasks of gene network inference from time-series data and 39 tasks of gene network inference from steady-state data. The results of the evaluation reveal that the association measures based on correlation combined with a particular scoring scheme of asymmetric weighting lead to optimal performance of the relevance network approach in the general case. In the two special cases of inference tasks involving short time-series data and/or large networks, association measures based on identifying qualitative trends in the time series are more appropriate.
DOI: 10.5524/100500
title: Supporting data for "Exploring the genome and transcriptome of the cave nectar bat Eonycteris spelaea with PacBio long-read sequencing"

description: In the past two decades, bats have emerged as an important model system to study host-pathogen interactions. More recently, it has been shown that bats may also serve as a new and excellent model to study aging, inflammation and cancer among other important biological processes. The cave nectar bat or lesser dawn bat (Eonycteris spelaea), is known to be a reservoir for several viruses and intracellular bacteria. It is a widely-distributed bat species throughout the tropics and subtropics from India to Southeast Asia, and pollinates several plant species, including the culturally and economically important durian in the region. Here, we report the whole-genome and transcriptome sequencing, followed by subsequent de novo assembly of the E. spelaea genome solely using the PacBio® long-read sequencing platform. <br>The newly assembled E. spelaea genome is 1.97 Gb in length and consists of 4,470 sequences with a contig N50 of 8.0 Mb. Identified repeat elements covered 34.65% of the genome and 20,640 unique protein coding genes with 39,526 transcripts were annotated. <br>We demonstrated that PacBio long-read sequencing platform alone is sufficient to generate a comprehensive de novo assembled genome and transcriptome of an important bat species. These results will provide useful insights and act as a resource to expand our understanding of bat evolution, ecology, physiology, immunology, viral infection and transmission dynamics.
DOI: 10.5524/100502
title: Genomic and Imaging Data Supporting the Digitization of Ruili Botanical Garden

description: Genome sequencing has been widely used in plant research to construct reference genomes and elucidate evolutionary insights. However, only a limited number of plant species have had their whole genome sequenced, and the limited taxon information of these species has further restrained the utility of these data. <br>Here, we comprehensively sampled and sequenced vascular plant species in and around Ruili Botanical Garden, located in South West China. We sequenced 761 samples out of the total 1,093 collected voucher specimens stored in the Herbarium of China National GeneBank (HCNGB). These 761 samples represented 689 vascular plant species from 137 families belonging to 49 orders. Of these, 257 samples were identified to the species level and 504 samples to the family level using specimens and chloroplast sequences. We generated 54 Tb sequencing data in total, which resulted in an average sequencing depth of 60× for these species, as estimated by the genome size. A reference phylogeny was reconstructed with 78 chloroplast genes for molecular identification and possible applications.<br>In this study, we established a large dataset of vascular plants genomes, with both the high-depth whole genome sequencing data and the voucher specimens, making it valuable dataset for plant genome researches and applications. And providing insight into the feasibility and technical requirements for planetary scale projects such as the 10 thousand Plant Genome Project (10KP) and Earth BioGenome Project (EBP).
DOI: 10.5524/100505
title: Supporting data for "Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism"

description: Trombidid mites have a unique lifecycle in which only the larval stage is ectoparasitic. In the superfamily Trombiculoidea ('chiggers'), the larvae feed preferentially on vertebrates, including humans. Species in the genus <i>Leptotrombidium</i> are vectors of a potentially fatal bacterial infection, scrub typhus, which affects 1 million people annually. Moreover, chiggers can cause pruritic dermatitis (trombiculiasis) in humans and domesticated animals. In the Trombidioidea (velvet mites), the larvae feed on other arthropods and are potential biological control agents for agricultural pests. Here, we present the first trombidid mites genomes, obtained both for a chigger, <i>Leptotrombidium deliense</i>, and for a velvet mite, <i>Dinothrombium tinctorium</i>.<br>Sequencing was performed using Illumina technology. A 180 Mb draft assembly for <i>D. tinctorium</i> was generated from two paired-end and one mate-pair library using a single adult specimen. For<i>L. deliense</i>, a lower-coverage draft assembly (117 Mb) was obtained using pooled, engorged larvae with a single paired-end library. Remarkably, both genomes exhibited evidence of ancient lateral gene transfer from soil-derived bacteria or fungi. The transferred genes confer functions that are rare in animals, including terpene and carotenoid synthesis. Thirty-seven allergenic protein families were predicted in the <i>L. deliense</i> genome, of which nine were unique. Preliminary proteomic analyses identified several of these putative allergens in larvae.<br>Trombidid mite genomes appear to be more dynamic than those of other acariform mites. A priority for future research is to determine the biological function of terpene synthesis in this taxon and its potential for exploitation in disease control.
DOI: 10.5524/100512
title: Supporting data for "An open-source high-speed infrared videography database to study the principles of active sensing in freely navigating rodents"

description: Active sensing is crucial for navigation. It is characterized by self-generated motor action controlling the accessibility and processing of sensory information. In rodents, active sensing is commonly studied in the whisker system. As rats and mice modulate their whisking contextually, they employ frequency and amplitude modulation. Understanding the development, mechanisms and plasticity of adaptive motor control will require precise behavioral measurements of whisker position. Advances in high-speed videography and analytical methods now permit collection and systematic analysis of large datasets. Here we provide 6642 videos as freely moving juvenile (3rd-4th postnatal week) and adult rodents explore a stationary object on the gap-crossing task. The dataset includes sensory exploration with single- or multi-whiskers in wild-type animals, serotonin transporter knock-out rats, rats received pharmacological intervention targeting serotonergic signaling. The dataset includes varying background illumination conditions and signal-to-noise ratios (SNRs), ranging from homogenous/high contrast to non-homogenous/low-contrast. A subset of videos has been whisker and nose tracked, and are provided as reference for image processing algorithms. The recorded behavioral data can be directly used to study (1) development of sensorimotor computation, (2) top-down mechanisms that control sensory navigation and whisker position, (3) cross-species comparison of active sensing. It could also help to address contextual modulation of active sensing during touch induced whisking in head-fixed versus freely behaving animals. And finally, it provides the necessary data for machine learning approaches for automated analysis of sensory and motion parameters across a wide variety of SNRs with accompanying human observer determined ground-truth.
DOI: 10.5524/100669
title: Supporting data for "De novo assembly of the cattle reference genome with single-molecule sequencing"

description: Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the <i>Bos taurus</i> reference genome (UMD3.1.1), which was created using now-outdated technologies and suffers from a variety of deficiencies and inaccuracies. We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a <i>de novo</i> assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb, and is &gt;250x more continuous than the original assembly, with contig N50 &gt;25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.