cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100865
title: Supporting data for "Comparative analysis of seven short-reads sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing"

description: MGISEQ-T7 is a new whole-genome sequencer developed by Complete Genomics and MGI utilizing DNA nanoball and combinatorial probe anchor synthesis technologies to generate short reads at a very large scale up to 60 human genomes per day. However, it has not been objectively and systematically compared against Illumina short-read sequencers. By using the same KOREF sample, the Korean Reference Genome, we have compared seven sequencing platforms including BGISEQ-500, MGISEQ-T7, HiSeq2000, HiSeq2500, HiSeq4000, HiSeqX10, and NovaSeq6000. We measured sequencing quality by comparing sequencing statistics (base quality, duplication rate, and random error rate), mapping statistics (mapping rate, depth distribution, and %GC coverage), and variant statistics (transition/transversion ratio, dbSNP annotation rate, and concordance rate with SNP genotyping chip) across the seven sequencing platforms. We found that MGI platforms showed a higher concordance rate for SNP genotyping than HiSeq2000 and HiSeq4000. The similarity matrix of variant calls confirmed that the two MGI platforms have the most similar characteristics to the HiSeq2500 platform.
DOI: 10.5524/100868
title: A chromosome‐level genome of the spider <i>Trichonephila antipodiana</i>

description: The spider <i>Trichonephila antipodiana</i> (Araneidae), commonly known as the batik golden web spider, preys on arthropods with body sizes ranging from approximately 2 mm in length to insects larger than itself (over 20 50 mm), indicating its polyphagy and strong dietary detoxification abilities. Although it has been reported that an ancient whole-genome duplication event occurred in spiders, lack of a high-quality genome has limited characterization of this event. We present a chromosomelevel <i>T. antipodiana</i> genome constructed based on PacBio and Hi-C sequencing. The assembled genome is 2.29 Gb in size with a scaffold N50 of 172.89 Mb. HiC scaffolding assigned 98.5% of the bases to 13 pseudo-chromosomes, and BUSCO completeness analysis revealed that the assembly included 94.8% of the complete arthropod universal single-copy orthologs (n=1,066). Repetitive elements account for 59.21% of the genome. We predicted 19,001 protein-coding genes, of which 96.78% were supported by transcriptome-based evidence and 96.32% matched protein records in the UniProt database. The genome also shows substantial expansions in several detoxification-associated gene families, including cytochrome P450 monooxygenases, carboxyl/cholinesterases, glutathione-S-transferases, and ATP-binding cassette transporters, reflecting the possible genomic basis of polyphagy. Further analysis of the <i>T. antipodiana</i> genome architecture reveals an ancient whole-genome duplication event, based on two lines of evidence: (1) large-scale duplications from inter-chromosome synteny analysis; (2) duplicated clusters of Hox genes. The high-quality <i>T. antipodiana</i> genome represents a valuable resource for spider research and provides insights into this species' adaptation to the environment.
DOI: 10.5524/100869
title: Supporting data for "epitopepredict: A tool for integrated MHC binding prediction"

description: A key step in the cellular adaptive immune response is the presentation of antigen to T cells. During this process, short peptides processed from self or foreign proteins may be presented on the surface-bound to MHC molecules for binding to T cell receptors. Those that bind and activate an immune response are called epitopes. Computational prediction of T cell epitopes has many applications in vaccine design and immuno-diagnostics. This is the basis of immunoinformatics which allows <i>in silico</i> screening of peptides before experiments are performed. The most effective approach is to estimate the binding affinity of a given peptide fragment to MHC class I or II molecules. With the availability of whole genomes for many microbial species, it is now feasible to computationally screen whole proteomes for candidate peptides. epitopepredict is a programmatic framework and command-line tool designed to aid this process. It provides access to multiple binding prediction algorithms under a single interface and scales for whole genomes using multiple target MHC alleles. A web interface is provided to assist visualization and filtering of the results. The software is freely available under an open-source license from GitHub.
DOI: 10.5524/100870
title: Supporting data for "Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines"

description: Sequencing of patient-derived xenograft (PDX) mouse models allows investigation of the molecular mechanisms of human tumor samples engrafted in a mouse host. Thus, both human and mouse genetic material is sequenced. Several methods have been developed to remove mouse sequencing reads from RNA-seq or exome sequencing PDX data and improve the downstream signal. However, for more recent chromatin conformation capture technologies (Hi-C), the effect of mouse reads remains undefined. We evaluated the effect of mouse read removal on the quality of Hi-C data using <i>in silico</i> created PDX Hi-C data with 10% and 30% mouse reads. Additionally, we generated two experimental PDX Hi-C datasets using different library preparation strategies. We evaluated three alignment strategies (Direct, Xenome, Combined) and three pipelines (Juicer, HiC-Pro, HiCExplorer) on Hi-C data quality. Removal of mouse reads had little-to-no effect on data quality than the results obtained with the Direct alignment strategy. Juicer extracted more valid chromatin interactions for Hi-C matrices, regardless of the mouse read removal strategy. However, the pipeline effect was minimal, while the library preparation strategy had the largest effect on all quality metrics. Together, our study presents comprehensive guidelines on PDX Hi-C data processing.
DOI: 10.5524/100871
title: High-quality <i>de novo</i> genome from an ethanol-preserved specimen of <i>Sminthurides aquaticus</i>

description: Genome sequencing of all known eukaryotes on Earth promises unprecedented advances in biological sciences and in biodiversity-related applied fields such as environmental management and natural product research. Advances in long read DNA sequencing make it feasible to generate high-quality genomes for many non-genetic model species. However, long read sequencing today relies on sizable quantities of high-quality, high molecular weight (hmw) DNA which is mostly obtained from fresh tissues. This is a challenge for biodiversity genomics of most metazoan species, which are tiny and need to be preserved immediately after collection. Here we present a de novo genome from an ethanol-preserved specimen of <i>Sminthurides aquaticus</i>. For this genome assembly, we prepared the sequencing library from hmw DNA extracted from a single specimen and using a novel Ultra-Low input protocol from Pacific Biosciences. This protocol requires a DNA input of only 5 ng, permitted by a whole genome amplification step. The assembled genome has a N50 value over 8.5 Mb and contains ~96% of BUSCO genes. Thus, this genome assembly is highly contiguous and complete. This species is devoid of the biosynthetic pathway for beta-lactam antibiotics known in several <i>Collembola</i>, confirming the tight correlation of antibiotics synthesis with the species way of life. It is now possible to generate high-quality genomes from single-specimens of minute, field-preserved metazoans, exceeding the minimum contig N50 (1Mb) required by the Earth BioGenome Project.
DOI: 10.17044/scilifelab.12771614.v1
title: HASTE miniTEM Example Images

description: Series of images of a sample of kidney tissue captured from the miniTEM (a 25keV transmission electron microscope) at Vironova offices in Stockholm (2019-02-04), for purposes of testing software related to the HASTE project (http://haste.research.it.uu.se/).<br>The dataset consists of 759 8-bit greyscale PNG images.<br><br>Used in this publication (and others):<br>Resource- and Message Size-Aware Scheduling of Stream Processing at the Edge with application to Realtime MicroscopyBen Blamey, Ida-Maria Sintorn, Andreas Hellander, Salman Toorhttps://arxiv.org/abs/1912.09088<br>Also"Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit, <em>GigaScience</em>, Volume 10, Issue 3, March 2021, giab018, https://doi.org/10.1093/gigascience/giab018<br>
DOI: 10.17044/scilifelab.12811997.v1
title: Snat10 Knockout Mice Cortical Neuronal Cells (ImageXpress XLS Example Images)

description: Image set collected in the Spjuth Lab (https://pharmb.io/), used as a test dataset for the HASTE software tools, and referenced in associated publications.<br>The images are of Snat10 knockout mice cortical neuronal cells, grown for 7 days and treated with either hydrogen peroxide or glutamate.<br>In total, there are 2699 TIFF images, organized by wavelength.<br>Images were taken with an ImageXpress XLS, at the Spjuth Lab.<br>All the archives decompress into this path:./181214-KOday7-40X-H2O2-Glu/2018-12-14/9/*.tif
DOI: 10.5524/100819
title: Supporting data for "Trajectories, bifurcations and pseudotime in large clinical datasets: applications to myocardial infarction and diabetes data"

description: Large observational clinical datasets become increasingly available for mining associations between various disease traits and administered therapy. These datasets can be considered as representations of the landscape of all possible disease conditions, in which a concrete pathology develops through a number of stereotypical routes, characterized by `points of no return' and `final states' (such as lethal or recovery states). Extracting this information directly from the data remains challenging, especially in the case of synchronic (with a short-term follow up) observations. Here we suggest a semi-supervised methodology for the analysis of large clinical datasets, characterized by mixed data types and missing values, through modeling the geometrical data structure as a bouquet of bifurcating clinical trajectories. The methodology is based on application of elastic principal graphs which can address simultaneously the tasks of dimensionality reduction, data visualization, clustering, feature selection and quantifying the geodesic distances (pseudotime) in partially ordered sequences of observations. The methodology allows positioning a patient on a particular clinical trajectory (pathological scenario) and characterizing the degree of progression along it with a qualitative estimate of the uncertainty of the prognosis. Overall, our pseudotime quantification-based approach gives a possibility to apply the methods developed for dynamical disease phenotyping and illness trajectory analysis (diachronic data analysis) to synchronic observational data. We developed a tool ClinTrajan for clinical trajectory analysis implemented in Python programming language. We test the methodology in two large publicly available datasets: myocardial infarction complications and readmission of diabetic patients data.
DOI: 10.5524/100821
title: Supporting data for "A New and Improved Genome Sequence of Cannabis sativa"

description: <i>Cannabis</i> is a diploid species (2n = 20), the estimated haploid genome sizes of the female and male plants using flow cytometry are 818 and 843 Mb respectively. Although the genome of <i>Cannabis</i> has been sequenced (from hemp, wild and high-THC strains), all assemblies have significant gaps. In addition, there are inconsistencies in the chromosome numbering which limits their use. A new comprehensive draft genome sequence assembly (~900 Mb) has been generated from the medicinal <i>Cannabis</i> strain Cannbio-2, that produces a balanced ratio of cannabidiol and delta-9-tetrahydrocannabinol using long-read sequencing. The assembly was subsequently analysed for completeness by ordering the contigs into chromosome-scale pseudomolecules using a reference genome assembly approach, annotated and compared to other existing reference genome assemblies. The Cannbio-2 genome sequence assembly was found to be the most complete genome sequence available based on nucleotides assembled and BUSCO evaluation in <i>Cannabis sativa</i> with a comprehensive genome annotation. The new draft genome sequence is an advancement in <i>Cannabis</i> genomics permitting pan-genome analysis, genomic selection as well as genome editing.
DOI: 10.5524/100823
title: Supporting data for "Chromosomal genome of Triplophysa bleekeri provides insights into its evolution and environmental adaptation"

description: Intense stresses caused by high-altitude environments may result in noticeable genetic adaptions in native species. Studies of genetic adaptations to high elevations have been largely limited to terrestrial animals. How fish adapt to the high-elevation environments is largely unknown. <i>Triplophysa bleekeri</i>, an endemic fish inhabiting high-altitude regions, presents an excellent model to investigate the genetic mechanisms of adaptation to the local environment. Here, we assembled a chromosomal genome sequence of about 628 Mb with a contig and scaffold N50 of 3.1 and 22.9 Mb, respectively. We investigated the origin and environmental adaptation of <i>T. bleekeri</i> based on 21,198 protein-coding genes in the genome. Compared to fish species living at low altitudes, gene families associated with lipid metabolism and immune response were significantly expanded in the <i>T. bleekeri</i> genome. Genes involved in DNA repair exhibit positive selection for <i>T. bleekeri</i>, <i>T. siluroides</i>, and <i>T. tibetana</i>, indicating that adaptive convergence in <i>Triplophysa</i> species occurred at the positively selected genes. We also analyzed whole-genome variants among samples from three populations. The results showed that populations separated by geological and artificial barriers exhibited obvious differences in genetic structures, indicating that gene flow is restricted between populations. These results will help us expand our understanding of environmental adaptation and genetic diversity of <i>T. bleekeri</i>, and provide valuable genetic resources for future studies on the evolution and conservation of high-altitude fish species such as <i>T. bleekeri</i>
DOI: 10.5524/100837
title: Supporting data for "Chromosome-level reference genome of the European wasp spider <i>Argiope bruennichi</i>: a resource for studies on range expansion and evolutionary adaptation"

description: <i>Argiope bruennichi</i>, the European wasp spider, has been investigated intensively as a focal species for studies on sexual selection, chemical communication, and the dynamics of rapid range expansion at a behavioral and genetic level. However, the lack of a reference genome has limited insights into the genetic basis for these phenomena. Therefore, we assembled a high-quality chromosome-level reference genome of the European wasp spider as a tool for more in-depth future studies. We generated, <i>de novo</i>, a 1.67Gb genome assembly of <i>A. bruennichi</i> using 21.8X PacBio sequencing, polished with 19.8X Illumina paired-end sequencing data, and proximity ligation (Hi-C) based scaffolding. This resulted in an N50 scaffold size of 124Mb and an N50 contig size of 288kb. We found 98.4% of the genome to be contained in 13 scaffolds, fitting the expected number of chromosomes (n = 13). Analyses showed the presence of 91.1% of complete arthropod BUSCOs, indicating a high quality assembly. We present the first chromosome-level genome assembly in the order Araneae. With this genomic resource, we open the door for more precise and informative studies on evolution and adaptation not only in <i>A. bruennichi</i>, but also in arachnids overall, shedding light on questions such as the genomic architecture of traits, whole-genome duplication and the genomic mechanisms behind silk and venom evolution.
DOI: 10.5524/100839
title: Supporting data for "Multiple origins of a frameshift insertion in a mitochondrial gene in birds and turtles"

description: During evolutionary history, molecular mechanisms have emerged to cope with deleterious mutations. Frameshift insertions in protein coding sequences are extremely rare because they disrupt the reading frame. There are a few known examples of their correction through translational frameshifting, a process which enables ribosomes to skip nucleotides during translation to regain proper reading frame. Corrective frameshifting has been proposed to act on the single base pair insertion at position 174 of the mitochondrial NADH dehydrogenase subunit 3 gene (ND3) that has been observed in several turtles and birds. However, the relatively sparse taxonomic representation has hampered our understanding on the evolution of this insertion in vertebrates.<br>Here, we analyzed 87,707 ND3 sequences from 10,308 vertebrate taxa to reveal the evolutionary history of this insertion and its common genomic characteristics. We confirmed that the insertion only appears in turtles and birds and reconstructed that it evolved independently in both groups with complex patterns of gains and losses. The insertion was observed in almost all bird orders but was absent in all members of the diverse Passeriformes. We found strong conservation in the nucleotides surrounding the insertion in both turtles and birds, which implies that the insertion enforces structural constraints that could be involved in its correction.<br>Our study demonstrates that frameshifts can be widespread, with complex patterns of gains and losses within birds and turtles and can be retained for millions of years if they are embedded in a conserved sequence theme.
DOI: 10.5524/100842
title: Supporting data for "A microbial gene catalog of anaerobic digestion from full-scale biogas plants"

description: Biogas production with anaerobic digestion (AD) is one of the most promising solutions for both renewable energy production and resolving the environmental problem caused by the increase in organic wastes worldwide. However, the complex structure of the microbiome in AD is less understood.<br>In this study, we constructed a microbial gene catalog of AD (22,840,185 genes), based on 1,817 gigabase (Gb) metagenomic data, derived from digestate samples of 56 full-scale biogas plants fed with diverse feedstocks. Among the gene catalog, 73.63% and 2.32% of genes were taxonomically annotated to Bacteria and Archaea, respectively and 57.07% of genes were functionally annotated with KEGG orthologous groups. Our results confirmed the existence of core microbiome in AD, and showed that the type of feedstock (cattle, chicken and pig manure) has a great influence on carbohydrate hydrolysis and methanogenesis. In addition, 2,426 metagenome-assembled genomes (MAGs) were recovered from all digestate samples, and all genomes were estimated to be 80% complete 10% contamination.<br>This study deepens our understanding of microbial compositions and functions in AD process, and also provides a huge number of reference genome and gene resources for analysis of anaerobic microbiota.
DOI: 10.5524/100846
title: Supporting data for "The Gene Expression Deconvolution Interactive Tool (GEDIT): Accurate Cell Type Quantification from Gene Expression Data"

description: The cell type composition of heterogeneous tissue samples can be a critical variable in both clinical and laboratory settings. However, current experimental methods of cell type quantification (e.g. cell flow cytometry) are costly, time consuming, and can introduce bias. Computational approaches that infer cell type abundance from expression data offer an alternate solution. While these methods have gained popularity, most are limited to predicting hematopoietic cell types and do not produce accurate predictions for stromal cell types. Many of these methods are also limited to particular platforms, whether RNA-seq or specific microarrays. We present the Gene Expression Deconvolution Interactive Tool (GEDIT), a tool that overcomes these limitations, compares favorably with existing methods, and provides superior versatility. Using both simulated and experimental data, we extensively evaluate the performance of GEDIT and demonstrate that it returns robust results under a wide variety of conditions. These conditions include a variety of platforms (microarray and RNA-seq), tissue types (blood and stromal), and species (human and mouse). Finally, we provide reference data from eight sources spanning a wide variety of stromal and hematopoietic types in both human and mouse. This reference database allows the user to obtain estimates for a wide variety of tissue samples without having to provide their own data. GEDIT also accepts user submitted reference data, thus allowing the estimation of any cell type or subtype, provided that reference data is available.
DOI: 10.5524/100849
title: Supporting data for "High throughput microscopy reveals the impact of multifactorial environmental perturbations on colorectal cancer cell growth"

description: Colorectal cancer (CRC) mortality is principally due to metastatic disease, with the most frequent organ of metastasis being liver. Biochemical and mechanical factors residing in the tumor microenvironment (TME) are considered to play a pivotal role in metastatic growth and response to therapy. However, it is difficult to study the TME systematically due to a lack of fully controlled model systems that can be investigated in rigorous detail. We present a quantitative imaging dataset of CRC cell growth dynamics influenced by in vivo-mimicking conditions. They consist of tumor cells grown in various biochemical and biomechanical microenvironmental contexts. These contexts include varying oxygen and drug concentrations, and growth on conventional stiff plastic, softer matrices, and bioengineered acellular liver extracellular matrix (ECM). Growth rate analyses under these conditions were performed via the cell phenotype digitizer (CellPD). Our data indicate the growth of highly aggressive HCT116 cells is affected by oxygen, substrate stiffness, and liver ECM. In addition, hypoxia has a protective effect against oxaliplatin-induced cytotoxicity on plastic and liver ECM. This expansive data set of CRC cell growth measurements under <i>in situ</i> relevant environmental perturbations provides insights into critical TME features contributing to metastatic seeding and tumor growth. Such insights are essential to dynamical modeling and understanding the multicellular tumor-stroma dynamics that contribute to metastatic colonization. It also establishes a benchmark data set for training and testing data-driven dynamical models of cancer cell lines and therapeutic response in a variety of microenvironmental conditions.