cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100595
title: Supporting data for "BSA4Yeast: Web-based QTL linkage analysis and bulk segregant analysis of yeast sequencing data"

description: Quantitative Trait Loci (QTL) mapping using bulk segregants is an effective approach for identifying genetic variants associated with phenotypes of interest in model organisms. By exploiting next-generation sequencing technology, the QTL mapping accuracy can be improved significantly, providing a valuable means to annotate new genetic variants. However, setting up a comprehensive analysis framework for this purpose is a time-consuming and error prone task, posing many challenges for scientists with limited experience in this domain. Here, we present BSA4Yeast, a comprehensive web-application for QTL mapping via bulk segregant analysis of yeast sequencing data. The software provides an automated and efficiency-optimized data processing, up-to-date functional annotations, and an interactive web-interface to explore identified QTLs. BSA4Yeast enables researchers to identify plausible candidate genes in QTL regions efficiently in order to experimentally validate causative genetic variations for a phenotype of interest. BSA4Yeast is freely available at https://bsa4yeast.lcsb.uni.lu.
DOI: 10.5524/100599
title: Supporting data for "LION/web: a web-based ontology enrichment tool for lipidomic data analysis"

description: A major challenge for lipidomic analyses is the handling of the large amounts of data and the translation of results to interpret the involvement of lipids in biological systems. We built a new lipid ontology (LION) that associates over 50,000 lipid species to biophysical, chemical and cell biological features. By making use of enrichment algorithms, we used LION to develop a web-based interface (LION/web, www.lipidontology.com) that allows identification of lipid-associated terms in lipidomes. LION/web was validated by analyzing a lipidomic dataset derived from well-characterized sub-cellular fractions of RAW 264.7 macrophages. Comparison of isolated plasma membranes with the microsomal fraction showed a significant enrichment of relevant LION-terms including plasma membrane, headgroup with negative charge, glycerophosphoserines, above average bilayer thickness, and below average lateral diffusion. A second validation was performed by analyzing the membrane fluidity of CHO cells incubated with arachidonic acid. An increase in membrane fluidity was observed both experimentally by using pyrene decanoic acid and by using LION/web, showing significant enrichment of terms associated with high membrane fluidity ('above average, 'very high and 'high lateral diffusion, and 'below average transition temperature). The results demonstrate the functionality of LION/web, which is freely accessible in a platform-independent way.
DOI: 10.5524/100600
title: Supporting data for "A large interactive visual database of copy number variants discovered in taurine cattle"

description: Copy number variants (CNVs) contribute to genetic diversity and phenotypic variation. We aimed to discover CNVs in taurine cattle using a large collection of whole-genome sequences and to provide an interactive database of the identified CNV regions (CNVRs) that includes visualisations of sequence read alignments, CNV boundaries and genome annotations.<br> CNVs were identified in each of four whole genome sequencing datasets, which together represent over 500 bulls from 17 breeds, using a popular multi-sample readdepth based algorithm, cn.MOPS. Quality control and CNVR construction, performed dataset-wise to avoid batch effects, resulted in a total of 26,223 CNVRs covering 107.75 unique megabases (4.05%) of the bovine genome. Hierarchical clustering of samples by CNVR genotypes indicated clear separation by breeds. An interactive HTML database was created that allows data filtering options, provides graphical and tabular data summaries including Hardy-Weinberg equilibrium tests on genotype proportions, and displays genes and quantitative trait loci at each CNVR. Notably, the database provides sequence read alignments at each CNVR genotype and the boundaries of constituent CNVs in individual samples. Besides numerous novel discoveries, we corroborated the genotypes reported for a CNVR at the KIT locus known to be associated with the piebald coat colour phenotype in Hereford and some Simmental cattle.<br> We present a large comprehensive collection of taurine cattle CNVs in a novel interactive visual database that displays CNV boundaries, read depths and genome features for individual CNVRs, thus providing users with a powerful means to explore and scrutinise CNVRs of interest more thoroughly.
DOI: 10.7488/ds/2513
title: Photometric stereo test data set

description: A test data set for extracting trait data from Arabidopsis thaliana plants using PS-Plant software. The data set included raw and processed data, and a pre-trained Mask R-CNN model. This data set forms part of work done in the BBSRC Tools and Resources Development project BB/N02334X/1. All PS-Plant software packages are available for download (https://bit.ly/2EFOk0O). Installation instructions are available on YouTube: https://youtu.be/7q6ZnJvhx6I. The PS-Plant software pipeline has seven steps: (1) PS data acquisition, (2) adaptive light source generation, (3) raw PS data processing, (4) rosette and (5) individual leaf mask generation, and (6) leaf instance tracking. The generation of compiled results (i.e. plant trait data) can be done at steps 4 and 6 to obtain rosette- and leaf-level data, respectively. Most PCs with onboard GPUs can be used to acquire and process PS data (steps 1-4 and 6). We recommend a PC with at least an Intel Core i3 equivalent CPU, and 4 GB of RAM. A GPU with a minimum Compute Unified Device Architecture (CUDA) capability of 3.5 (https://bit.ly/1Jnzfz8) is required for the generation of leaf masks (step 5) using the Leaf Segmentation GUI.
DOI: 10.7488/ds/2514
title: Photometric stereo training data set with annotated leaf masks
title: Photometric stereo dataset with annotated leaf masks

description: Automated leaf segmentation is a challenging area in computer vision. Recent advances in machine learning approaches allowed to achieve better results than traditional image processing techniques; however, training such systems often require large annotated data sets. To contribute with annotated data sets and help to overcome this bottleneck in plant phenotyping research, here we provide a novel photometric stereo (PS) data set with annotated leaf masks. This data set forms part of work done in the BBSRC Tools and Resources Development project BB/N02334X/1.
DOI: 10.5524/100570
title: Supporting data for "An efficient and improved laboratory workflow and tetrapod database for larger scale eDNA studies"

description: The use of environmental DNA, eDNA, for species detection via metabarcoding is growing rapidly and now, even terrestrial mammals can be monitored via invertebrate-derived DNA or iDNA from hematophagous invertebrates. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the two most important risks of e/iDNA: sample contamination and taxonomic mis-assignment. These risks arise from the need for amplification to detect the trace amounts of DNA and the necessity of using short target regions due to DNA degradation. Here we present a high-throughput laboratory workflow that minimises these risks via a three-step strategy: (1) each sample is sequenced for two PCR replicates from each of two extraction replicates; (2) we use a twin-tagging, two-step PCR protocol; (3) and a multi-marker approach targeting three mitochondrial loci: 12S, 16S and CytB. As a test, 1532 leeches were analysed from Sabah, Malaysian Borneo. Twin-tagging allowed us to detect and exclude chimeric sequences. The smallest DNA fragment (16S) amplified best for all samples but often at lower taxonomic resolution. We only accepted assignments that were found in both extraction replicates, totalling 174 assignments for 96 samples. To avoid false taxonomic assignments, we also present an approach to create curated reference databases that can be used with the powerful taxonomic-assignment method PROTAX. For some taxonomic groups and some markers, curation resulted in over 50% of sequences being deleted from public reference databases, due mainly to: (1) limited overlap between our target amplicon and available reference sequences; (2) apparent mislabelling of reference sequences; (3) redundancy. A provided bioinformatics pipeline processes amplicons and conducts the PROTAX taxonomic assignment. Our metabarcoding workflow should help research groups to increase the robustness of their results and therefore facilitate wider usage of e/iDNA, which is turning into a valuable source of ecological and conservation information on tetrapods.
DOI: 10.5524/100573
title: Supporting data for "Datastorr: a workflow and package for delivering successive versions of 'evolving data' directly into R"

description: The sharing and re-use of data has become a cornerstone of modern science. Multiple platforms now allow quick and easy data sharing. So far, however, data publishing offers limited functions for interacting with evolving datasets - those that continue to grow with time as more records are added, errors fixed, and new data structures are created. In this article, we describe a workflow for maintaining and distributing successive versions of an evolving dataset, allowing users to retrieve and load different versions directly into the R platform. Our workflow utilises tools and platforms used for development and distribution of successive versions of a open source software, including version control, GitHub and semantic versioning, and applies these to the analogous process of developing successive versions of an open source dataset. Moreover, we argue that this model allows for individual research groups to achieve a dynamic and versioned model of data delivery at no cost.
DOI: 10.5524/100577
title: Supporting data for "PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and miRNAs across 32 cancers"

description: Long thought "relics" of evolution, not until recently have pseudogenes been of medical interest regarding regulation in cancer. Often, these regulatory roles are a direct byproduct of their close sequence homology to protein coding genes. Novel pseudogene-gene functional associations can be identified through the integration of biomedical data, such as sequence homology, functional pathways, gene expression, pseudogene expression, and miRNA expression. However, not all of the information has been integrated, and the vast majority of previous pseudogene studies relied on 1:1 pseudogene-parent gene relationships without leveraging other homologous genes/pseudogenes. We produce pseudogene-gene (PGG) families that expand beyond the current 1:1 paradigm. Firstly, we construct expansive PGG databases by i) CUDAlign GPU accelerated local alignment of all pseudogenes to gene families (totaling 1.6 billion individual local alignments and more than 40,000 GPU hours) and ii) BLAST-based assignment of pseudogenes to gene families. Secondly, we create an open-source web application (PseudoFuN) to search for integrative functional relationships of sequence homology, miRNA expression, gene expression, pseudogene expression, and gene ontology. We produce four "flavors" of databases (&gt;462,000,000 pseudogene-gene pairwise alignments and 133,770 PGG families) that can be queried and downloaded using PseudoFuN. These databases are consistent with previous 1:1 pseudogene-gene annotation and also are much more powerful including millions of de novo pseudogene-gene associations. For example, we find multiple known (e.g., miR-20a-PTEN-PTENP1) and novel (e.g., miR-375-SOX15- PPP4R1L) miRNA-gene-pseudogene associations in prostate cancer. PseudoFuN provides a "one stop shop" for identifying and visualizing thousands of potential regulatory relationships related to pseudogenes in TCGA cancers. Thousands of new pseudogene-gene associations can be explored in the context of miRNA-gene-pseudogene co-expression and differential expression with a simple-to-use online tool by bioinformaticians and oncologists alike.
DOI: 10.5524/100581
title: Supporting data for "Microbiome Learning Repo (ML Repo): A public repository of microbiome regression and classification tasks"

description: The use of machine learning in high-dimensional biological applications, such as the human microbiome, has grown exponentially in recent years, but algorithm developers often lack domain expertise required for interpretation and curation of the heterogeneous microbiome datasets. We present Microbiome Learning Repo (ML Repo, available at https://knights-lab.github.io/MLRepo/), a public, web-based repository of 33 curated classification and regression tasks from 15 published human microbiome datasets. We highlight the use of ML Repo in several use cases to demonstrate its wide application, and expect it to be an important resource for algorithm developers.
DOI: 10.5524/100588
title: Supporting data for "Map and Model – moving from observation to prediction in toxicogenomics"

description: Chemicals induce compound specific changes on the transcriptome of an organism (toxicogenomic finngerprints). This provides potential insights about the cellular or physiological responses to chemical exposure and adverse effects, which is needed in assessment of chemical related hazards or environmental health. In this regard, comparison or connection of dfferent experiments becomes important when interpreting toxicogenomic experiments. Due to lack of capturing response dynamics, comparability is often limited. In this study, we aim to overcome these constraints. <br>We developed an experimental design and bioinformatic analysis strategy to infer time and concentration-resolved toxicogenomic fingerprints. We projected the fingerprints to a universal coordinate system (toxicogenomic universe), based on a self-organizing map of toxicogenomic data retrieved from public databases. Genes clustering together in regions of the map indicate functional relation due to co-expression under chemical exposure. To allow for quantitative description and extrapolation of the gene-expression responses we developed a time and concentration-dependent regression model.<br> We applied the analysis strategy in a microarray case study exposing zebrafish embryos to three selected model compounds including two cyclooxygenase inhibitors. After identification of key responses in the transcriptome we could compare and characterise their association to developmental, toxicokinetic, and toxicodynamic processes using the parameter estimates for affected gene clusters. Furthermore, we discuss an association of toxicogenomic effects with measured internal concentrations. The design and analysis pipeline described here could serve as a blueprint for creating comparable toxicogenomic fingerprints of chemicals. It integrates, aggregates, and models time and concentration-resolved toxicogenomic data.
DOI: 10.5524/100590
title: Supporting data for "An integrated chromosome-scale genome assembly of the Masai Giraffe (Giraffa camelopardalis tippelskirchi)"

description: The Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the worlds tallest terrestrial animal. With its extreme size and height, the giraffes unique anatomical and physiological adaptations have long been of interest to diverse research fields. Giraffes are also critical to ecosystems of sub-Saharan Africa, with their long neck serving as a conduit to food sources not shared by other herbivores. Although the genome of a Masai giraffe has been sequenced, the assembly was highly fragmented and unsuitable for the analysis of chromosome evolution. Herein we report an improved giraffe genome assembly to facilitate evolutionary analysis of the giraffe and other ruminant genomes.<br>Using SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads we generated a 2.6 Gbp female Masai giraffe genome assembly, with a scaffold N50 of 3 Mbp. The incorporation of 114.6 Gbp of Chicago library sequencing data resulted in a HiRise SOAPdenovo + Chicago assembly with an N50 of 48 Mbp and containing 95% of expected genes according to BUSCO analysis. Using the Reference-Assisted Chromosome Assembly tool, we were able to order and orient scaffolds into 42 predicted chromosome fragments (PCFs). Using fluorescence in situ hybridization we hybridized 153 cattle BACs onto giraffe metaphase spreads to assess and place the PCFs on 14 giraffe autosome and 10 sex chromosome fragments. In this assembly, 21,621 protein-coding genes were identified and 1 Gbp of repetitive sequences annotated using both de novo and homology-based predictions.<br>Our results provide the first chromosome-scale genome assembly for the Masai giraffe. This assembly will be a valuable tool to elucidate the evolution and molecular basis of adaptive traits of the Giraffidae, and will provide a new genomic resource to assist conservation efforts.
DOI: 10.5524/100611
title: Supporting data for "iMicrobe: Tools and data-driven discovery platform for the microbiome sciences"

description: Scientists have amassed a wealth of microbiome datasets making it possible to study microbes in biotic and abiotic systems on a population- or planetary-scale; however, this potential hasnt been fully realized given that the tools, data sets, and computation are available in diverse repositories and locations. To address this challenge, we developed iMicrobe.us, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community.<br>The iMicrobe platform brings together analysis tools and microbiome data sets by leveraging National Science Foundation-supported cyberinfrastructure and computing resources from CyVerse, Agave, and XSEDE. The primary purpose of iMicrobe is to provide users with a freely available, web-based platform to (1) maintain and share project data, metadata, and analysis products, (2) search for related public datasets, and (3) use and publish bioinformatics tools that run on highly-scalable computing resources. Analysis tools are implemented in containers that encapsulate complex software dependencies and run on freely available XSEDE resources via the Agave API which can retrieve datasets from the CyVerse Data Store or any web-accessible location (e.g., FTP, HTTP).<br>iMicrobe promotes data integration, sharing, and community-driven tool development by making open source data and tools accessible to the research community in a webbased platform.
DOI: 10.5524/100567
title: Supporting data for "Single-cell Transcriptomic Landscape of Nucleated Cells in Umbilical Cord Blood"

description: Umbilical cord blood (UCB) transplant is a therapeutic option for both pediatric and adult patients with a variety of hematologic diseases such as several types of blood cancers, myeloproliferative disorders, genetic diseases, and metabolic disorders. However, the level of cellular heterogeneity and diversity of nucleated cells in the UCB has not yet been assessed in an unbiased and systemic fashion. In the current study, nucleated cells from UCB were subjected to single-cell RNA sequencing, a technology enabled simultaneous profiling of the gene expression signatures of thousands of cells, generating rich resources for further functional studies. Here, we report the transcriptome of 17,637 UCB cells, covering twelve major cell types. Many of these cell types are comprised of distinct subpopulations. Pseudotemporal ordering of nucleated red blood cells (NRBC) identifies wave-like activation and suppression of transcription regulators, leading to a polarized cellular state, which may reflect NRBC maturation. Progenitor cells in UCB also consist two subpopulations with divergent transcription programs activated, leading to specific cell-fate commitment. Detailed profiling of cytotoxic cell populations unveiled granzymes B and K signatures in NK and NKT cell types in UCB. Collectively, we provide this comprehensive single-cell transcriptomic landscape and show that it can uncover previously unrecognized cell types, pathways and gene expression regulations that may contribute to the efficacy and outcome of UCB transplant, broadening the scope of research and clinical innovations.
DOI: 10.5524/100571
title: Supporting data for "The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition"

description: Pecan (<i>Carya illinoinensis</i>) and Chinese hickory (<i>C. cathayensis</i>) are important commercially cultivated nut trees in genus Carya (Juglandaceae), with high nutritional value and significant health benefits. <br>We obtained more than 187.22 Gb and 178.87 Gb sequences, <i>~</i>288x and 248x genome coverage, to a pecan cultivar (Pawnee) and a domesticated Chinese hickory landrace (ZAFU-1). The total assembly is 651.31 Mb for pecan and 706.43 Mb for Chinese hickory. Two genome duplication events before the divergence from walnut were found in these species. Gene family analysis highlighted key genes in biotic and abiotic tolerance, oil, polyphenols, essential amino acids and B vitamins. Further analyses of reduced-coverage genome sequences of 16 Carya and 2 Juglans species provide additional phylogenetic perspective on crop wild relatives. <br>Cooperative characterization of these valuable resources provides a window to their evolutionary development, and a valuable foundation for future crop improvement.
DOI: 10.5524/100576
title: Supporting data for "De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers"

description: In recent years, massively parallel cDNA sequencing (RNA-Seq) has emerged as a fast, cost-effective and powerful technology to study entire transcriptomes in various manners. In particular, for non-model organisms and in the absence of an appropriate reference genome, RNA-Seq is used to reconstruct the transcriptome de novo. Although the de novo transcriptome assembly of non-model organism has been on the rise recently and new tools are developed frequently, there is still a knowledge gap about which assembly software should be used to build a comprehensive de novo assembly. Here we present a large-scale comparative study in which ten de novo assembly tools are applied to nine RNA-Seq data sets spanning different kingdoms of life. Overall, we build more than 200 single assemblies and evaluated their performance on a combination of 20 biological-based and reference-free metrics. Our study is accompanied by a comprehensive and extensible Electronic Supplement that summarizes all data sets, assembly execution instructions, and evaluation results. Trinity, SPAdes and Trans-ABySS, followed by Bridger and SOAPdenovo-Trans, generally outperformed the other tools compared. In addition, we observed species-specific differences in the performance of each assembler. No tool delivered the best results for all data sets. We recommend a careful choice and normalization of evaluation metrics to select the best assembling results as a critical step in the reconstruction of a comprehensive de novo transcriptome assembly.