cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102619
title: Supporting data for "Similar, but not the same: multi-omics comparison of human valve interstitial cells and osteoblast osteogenic differentiation expanded with an estimation of data-dependent and data-independent PASEF proteomic"

description: Osteogenic differentiation is crucial in normal bone formation and pathological calcification, such as calcific aortic valve disease (CAVD). Understanding the proteomic and transcriptomic landscapes underlying this differentiation can unveil potential therapeutic targets for CAVD. In this study, we employed RNA sequencing transcriptomics and proteomics on a timsTOF Pro platform to explore the multi-omics profiles of valve interstitial cells (VICs) and osteoblasts during osteogenic differentiation. For proteomics, we utilized three data acquisition/analysis techniques: Data-Dependent Acquisition (DDA-PASEF) and Data-Independent Acquisition (DIA-PASEF) with a classic library-based (DIA) and machine learning-based library-free search (DIA-ML). Using RNA-seq data as biological reference, we compared these three analytical techniques in the context of actual biological experiments. We use this comprehensive dataset to reveal distinct proteomic and transcriptomic profiles between VICs and osteoblasts, highlighting specific biological processes in their osteogenic differentiation pathways. The study identified potential therapeutic targets specific for VICs osteogenic differentiation in CAVD, including MAOA and ERK1/2 pathway. From a technical perspective, we found that DIA-based methods demonstrate even higher superiority against DDA for more sophisticated human primary cell cultures than it was shown before on HeLa samples. While the classic library-based DIA approach has proved to be a golden standard for shotgun proteomics research, the DIA-ML offers significant advantages with a relatively minor compromise in data reliability, making it the method of choice for routine proteomics.
DOI: 10.5524/102624
title: Supporting data for "scGraph2Vec: a deep generative model for gene embedding augmented by Graph Neural Network and single-cell omics data"

description: Exploring the cellular processes of genes from the aspects of biological networks is of great interest to understanding the properties of complex diseases and biological systems. Biological networks, such as protein-protein interaction networks and gene regulatory networks, provide insights into the molecular basis of cellular processes and often form functional clusters in different tissue and disease contexts. <br>We present scGraph2Vec, a deep-learning framework for generating informative gene embeddings. scGraph2Vec extends the variational graph autoencoder framework and integrates single-cell datasets and gene-gene interaction networks. We demonstrate that the gene embeddings are biologically interpretable and enable the identification of gene clusters representing functional or tissue-specific cellular processes. By comparing similar tools, we showed that scGraph2Vec clearly distinguished different gene clusters and aggregated more biologically functional genes. scGraph2Vec can be widely applied in diverse biological contexts. We illustrated that the embeddings generated by scGraph2Vec can infer disease-associated genes from genome-wide association study data (e.g., COVID-19 and Alzheimers Disease), identify additional driver genes in lung adenocarcinoma, and reveal regulatory genes responsible for maintaining or transitioning melanoma cell states. <br>scGraph2Vec not only reconstructs tissue-specific gene networks but also obtains a latent representation of genes implying their biological functions.
DOI: 10.5524/102626
title: Supporting data for "A chromosome-scale genome assembly of the pioneer plant Stylosanthes angustifolia: insights into genome evolution and drought adaptation"

description: Drought is a major limiting factor for plant survival and crop productivity. <i>Stylosanthes angustifolia</i>, a pioneer plant, exhibits remarkable drought tolerance, yet the molecular mechanisms driving its drought resistance remain largely unexplored.<br>We present a chromosome-scale reference genome of <i>S. angustifolia</i>, which provides insights into its genome evolution and drought tolerance mechanisms. The assembled genome is 645.88 Mb in size, containing 319.98 Mb of repetitive sequences and 36,857 protein-coding genes. The high quality of this genome assembly is demonstrated by the presence of 99.26% Benchmarking Universal Single-Copy Orthologs and a 19.49 LTR assembly index. Evolutionary analyses revealed that <i>S. angustifolia</i> shares a whole-genome duplication (WGD) event with other legumes but lacks recent WGD. Additionally, <i>S. angustifolia</i> has undergone gene expansion through tandem duplication approximately 12.31 million years ago. Through integrative multi-omics analyses, we identified four gene families, namely xanthoxin dehydrogenase, 2-hydroxyisoflavanone dehydratase, patatin-related phospholipase A, and stachyose synthetase, that underwent tandem duplication and were significantly up-regulated under drought stress. These gene families contribute to the biosynthesis of abscisic acid, genistein, daidzein, jasmonic acid, and stachyose, thereby enhancing drought tolerance.<br>The genome assembly of <i>S. angustifolia</i> represents a significant advancement in understanding the genetic mechanisms underlying drought tolerance in this pioneer plant species. This genomic resource provides critical insights into the evolution of drought resistance and offers valuable genetic information for breeding programs aimed at improving drought resistance in crops.
DOI: 10.5524/102631
title: Genome assembly of the musk deer <i>Moschus berezovskii</i> Flerov

description: The forest musk deer (<i>Moschus berezovskii</i>) is a small deer, measuring between 70 and 80 cm in height and weight between 6 and 9 kg. This species is endemic to the forest of Central and South Asia, with a notable presence in southern and central China. One of its most distinctive features is the musk gland, which is highly sought after in traditional medicine and the fragrance industry. <i>M. berezovskii</i> displays various morphological adaptations that facilitate its survival in challenging environments. Notably, males possess elongated canine teeth and lack antlers, setting them apart from true deer species. The diet of <i>M. berezovskii</i> is primarily herbivorous, consisting of diverse plant materials such as grasses and shrubs. In terms of reproductive behavior, this species exhibits a polygynous mating system, with a gestation period lasting approximately 6 to 7 months, typically resulting in the birth of a single offspring. Despite its ability to adapt, populations of musk deer are currently threatened by significant challenges, including habitat destruction from deforestation, poaching for their valuable musk, and competition with domesticated livestock. <br>We present a publicly available genome assembly of the musk deer <i>Moschus berezovskii</i>, with 696.2 Gb (~246 fold coverage) of sequence data. The complete assembly spans 2.8 Gb, with contig N50 of 69.4 Mb and scaffold N50 of 105.8 Mb anchored onto 30 chromosomes. The BUSCO analysis indicates a completeness of 96.28% (QV 44.09).
DOI: 10.5524/102633
title: Supporting data for "TransHLA: A Hybrid Transformer Model for HLA-Presented Epitope Detection"

description: Precise prediction of epitope presentation on human leukocyte antigen (HLA) molecules is crucial for advancing vaccine development and immunotherapy. Conventional HLA-peptide binding affinity prediction tools often focus on specific alleles and lack a universal approach for comprehensive HLA site analysis. This limitation hinders efficient filtering of invalid peptide segments. <br>We introduce TransHLA, a pioneering tool designed for epitope prediction across all HLA alleles, integrating Transformer and Residue CNN architectures. TransHLA utilizes the ESM2 large language model for sequence and structure embeddings, achieving high predictive accuracy. For HLA class I, it reaches an accuracy of 84.72% and an AUC of 91.95% on IEDB test data. For HLA class II, it achieves 79.94% accuracy and an AUC of 88.14%. Our case studies using datasets like CEDAR and VDJdb demonstrate that TransHLA surpasses existing models in specificity and sensitivity for identifying immunogenic epitopes and neoepitopes. <br>TransHLA significantly enhances vaccine design and immunotherapy by efficiently identifying broadly reactive peptides. Our resources, including data and code, are publicly accessible at https://github.com/SkywalkerLuke/TransHLA
DOI: 10.5524/102642
title: Supporting data for "Observational, Causal Relationship and Shared Genetic Basis Between Cholelithiasis and Gastroesophageal Reflux Disease: Evidence from a Cohort Study and Comprehensive Genetic Analysis"

description: Cholelithiasis and gastroesophageal reflux disease (GERD) contribute to significant health concerns. We aimed to investigate the potential observational, causal and genetic relationships between cholelithiasis and GERD. <br>The observational correlations were assessed based on the prospective cohort study from UK Biobank. Then, by leveraging the genome-wide summary statistics of cholelithiasis (N = 334,277) and GERD (N = 332,601), the bidirectional causal associations was evaluated using Mendelian randomization (MR) analysis. Subsequently, a series of genetic analyses was used to assess the genetic correlation, shared loci and genes between cholelithiasis and GERD. <br>The prospective cohort analyses revealed a significant increased risk of GERD in individuals with cholelithiasis (Hazard ratio (HR) = 1.99, 95% confidence interval (CI) = 1.89-2.10) and a higher risk of cholelithiasis among GERD patients (HR = 2.30, 95% CI = 2.18-2.44). The MR study indicated the causal effect of genetic liability to cholelithiasis on the incidence of GERD (Odds ratio (OR) = 1.07, 95% CI = 1.05-1.10) and the causal effect of genetic predicted GERD on cholelithiasis (IVW OR = 1.15, 95% CI = 1.02-1.30). Besides, cholelithiasis and GERD exhibited a strong genetic association. Cross-trait meta-analyses identified 5 novel independent loci shared between cholelithiasis and GERD. Three shared genes including <em>SUN2</em>, <em>CBY1</em>, and <em>JOSD1</em> were further identified as novel risk genes. <br>The elucidation of the shared genetic basis underlying the phenotypic relationship of these two complex phenotypes offers new insights into the intrinsic linkage between cholelithiasis and GERD, providing a novel research direction for future therapeutic strategy and risk prediction.
DOI: 10.5524/102645
title: Supporting data for "Exploring the Cellular and Molecular Basis of Murine Cardiac Development through Spatiotemporal Transcriptome Sequencing"

description: Spatial transcriptomics is a powerful tool that combines molecular data with spatial information, enabling a deeper understanding of tissue morphology and cellular interactions. In this study, we employed state-of-the-art spatial transcriptome sequencing technology to investigate the development of the mouse heart and establish a comprehensive spatiotemporal cell atlas of early murine cardiac development. Through the analysis of this atlas, we elucidated the spatial organization of cardiac cellular lineages and their interactions during development. Notably, we observed dynamic changes in gene expression within fibroblasts and cardiomyocytes. Furthermore, we identified critical genes including <i>Igf2</i>, <i>H19</i>, <i>Tcap</i>, as well as transcription factors of <i>Tcf12</i> and <i>Plagl1</i>, that may be associated with the loss of myocardial regeneration ability during early heart development. Moreover, we successfully identified marker genes, such as <i>Adamts8</i> and <i>Bmp10</i>, that can distinguish between the left and right atria. Our study provides novel insights into murine cardiac development and offers a valuable resource for future investigations in the field of heart research.
DOI: 10.5524/102601
title: Supporting data for "Whole-genome re-sequencing of the Baikal seal and other phocid seals for a glimpse into their genetic diversity, demographic history, and phylogeny"

description: The iconic Baikal seal (<i>Pusa sibirica</i>), the smallest true seal, is a freshwater seal that is endemic to Lake Baikal where it became landlocked some million years ago. It is a rather abundant species of least concern, despite the limited habitat. Until recently, research on its genetic diversity has only been done on mitochondrial genes, restriction fragment analyses, and microsatellites, before its reference genome has been published. <br>Here we report the genome sequences of six Baikal seals, and one individual of the Caspian seal, ringed seal, and the harbor seal, re-sequenced from Illumina paired-end short read data. Heterozygosity calculations of the six newly sequenced individuals are like the previously reported genomes. In addition, the novel genome data of the other species contributed to a more complete phocid seal phylogeny based on whole-genome data. <br>Despite the long isolation of the land-locked Baikal seal population, the genetic diversity of this species is in the same range as other seal species. The Baikal seal appears to form a single, diverse population. However, targeted genome studies are needed to explore the genomic diversity throughout their distribution.
DOI: 10.5524/102609
title: Supporting data for "Chromosome-level echidna genome illuminates evolution of multiple-sex-chromosome system in monotremes"

description: A thorough analysis of genome evolution is fundamental for biodiversity understanding. The iconic monotremes (platypus and echidna) feature extraordinary biology but the lack of a chromosome-level echidna genome has limited insights into genome evolution in monotremes, in particular the multiple sex chromosomes complex. <br>Here, we present a new long-reads-based chromosome-level short-beaked echidna (<i>Tachyglossus aculeatus</i>) genome, which allowed the inference of chromosomal rearrangements in the monotreme ancestor (2n = 64) and each extant species. Analysis of the more complete sex chromosomes uncovered homology between one Y chromosome and multiple X chromosomes, suggesting that it is the ancestral X that has undergone reciprocal translocation with ancestral autosomes to form the complex. We also identified dozens of ampliconic genes on the sex chromosomes, with several ancestral ones expressed during male meiosis, suggesting selective constraints in pairing the multiple sex chromosomes. <br>The new echidna genome provides an important basis for further study of the unique biology and conservation of this species.
DOI: 10.5524/102610
title: Genome data of the cyprinid fish, <i>Culter alburans</i> (Topmouth Culter)

description: Topmouth culter (<i>Culter alburnus</i>), a carnivorous freshwater fish belonging to the Cyprinidae family, has garnered significant popularity in China, because of its distinctive flavor and rich nutritional value. Since the establishment of its aquaculture industry in 1999, <i>C. alburnus</i> has become a commercially valuable fish species with large market requirements. The natural populations of <i>C. alburnus</i> are found in major Chinese river systems such as the Heilongjiang, Yellow, Huai, Yangtze, and Pearl Rivers across the northern and southern parts of China. The diverse environmental settings within these river basins, including water characteristics and climatic element variations, have subjected the populations to selective pressures, resulting in evolutionary adaptations. [j.aqrep.2024]<br>Here we present a publicly available chromosome-scale genome assembly of the topmouth culter <i>C. alburnus</i>. The assembled genome spans 108 Mb and exhibits a scaffold N50 value of 39.60 Mb and a contig N50 of 18.55 (increased from 17.8 Mb). The BUSCO results indicated high genome assembly completeness, with 98.3% of single-copy core genes present. A total of 27,303 protein-coding genes were predicted, repetitive elements comprised 50.49% (544.26 Mb) of the assembly, and non-coding RNA was predicted in 7.21 of the genome.
DOI: 10.5524/102618
title: Supporting data for "ssMutPA: Single-sample Mutation-based Pathway Analysis approach for cancer precision medicine"

description: Single-sample pathway enrichment analysis is an effective approach for identifying cancer subtypes and pathway biomarkers, facilitating the development of precision medicine. However, the existing approaches focused on investigating the changes in gene expression levels but neglected somatic mutations which play a crucial role in cancer development. <br>In this study, we proposed a novel single-sample mutation-based pathway analysis approach (ssMutPA) to infer individualized pathway activities by integrating somatic mutation data and the protein-protein interaction (PPI) network. For each sample, ssMutPA first uses local and global weighted strategies to evaluate the effects of genes from mutations according to the network topology and then calculates a single-sample mutation-based pathway enrichment score (ssMutPES) to reflect the accumulated effect of mutations of each pathway. To illustrate the performance of ssMutPA, we applied it to 33 cancer cohorts from the TCGA database and revealed patient stratification with significantly different prognosis in each cancer type based on the ssMutPES profiles. We also found that the identified characteristic pathways with high overlap across different cancers could be used as potential prognosis biomarkers. Moreover, we applied ssMutPA to two melanoma cohorts with immunotherapy and identified a subgroup of patients who may benefit from therapy. <br>We provided evidence that ssMutPA could infer mutation-based individualized pathway activity profiles and complement the current individualized pathway analysis approaches focused on gene expression data, which may offer the potential for the development of precision medicine. ssMutPA is available at (https://CRAN.R-project.org/package=ssMutPA).
DOI: 10.5524/102623
title: Supporting data for "A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: <i>Phoxinus phoxinus</i>) provide evidence of haplotype diversity"

description: In this study we present an in-depth analysis of the Eurasian minnow (<i>Phoxinus phoxinus</i>) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated an annotated haplotype-phased, chromosome-level genome assembly (2n = 50) by integrating high-fidelity (HiFi) long reads and chromosome conformation capture data (Hi-C).<br>We achieved a haploid size of 940 Megabase pairs (Mbp) for haplome one and 929 Mbp for haplome two with high scaffold N50 values of 36.4 Mb and 36.6 Mb and BUSCO scores of 96.9% and 97.2%, respectively, indicating a highly complete genome assembly.<br>We detected notable heterozygosity (1.43%) and a high repeat content (approximately 54%), primarily consisting of DNA transposons, which contribute to genome rearrangements and variations. We found substantial structural variations within the genome, including insertions, deletions, inversions, and translocations. These variations affect genes enriched in functions such as dephosphorylation, developmental pigmentation, phagocytosis, immunity, and stress response.<br>In the annotation of protein-coding genes, 30,980 mRNAs and 23,497 protein-coding genes were identified with a high completeness score, which further underpins the high contiguity of our genome assemblies. We performed a gene family evolution analysis by comparing our proteome to ten other teleost species, which identified immune system gene families that prioritise histone-based disease prevention over NLR-based immune responses.<br>Additionally, demographic analysis indicates historical fluctuations in the effective population size of <i>P. phoxinus</i>, likely correlating with past climatic changes.<br>This annotated, phased reference genome provides a crucial resource for resolving the taxonomic complexity within the genus <i>Phoxinus</i> and highlights the importance of haplotype-phased assemblies in understanding haplotype diversity in species characterised by high heterozygosity.
DOI: 10.5524/102628
title: Supporting data for "Multi-omics analysis provides insights into musk secretion in muskrat and musk deer"

description: Musk, secreted by the musk gland of adult male musk-secreting mammals, holds significant pharmaceutical and cosmetic potential. However, understanding the molecular mechanisms of musk secretion remain limited, largely due to the lack of comprehensive multi-omics analyses and available platforms for relevant species, such as muskrat (<i>Ondatra zibethicus</i> Linnaeus) and Chinese forest musk deer (<i>Moschus berezovskii</i> Flerov). <br>We generated chromosome-level genome assemblies for the two species muskrat (<i>Ondatra zibethicus</i> Linnaeus) and musk deer (<i>Moschus berezovskii</i> Flerov), along with 168 transcriptomes from various muskrat tissues. Comparative analysis with eleven other vertebrate genomes revealed genes and amino acid sites with signs of adaptive convergent evolution, primarily linked to lipid metabolism, cell cycle regulation, protein binding, and immunity. Single-cell RNA sequencing in muskrat musk glands identified increased acinar/glandular epithelial cells during secretion, highlighting the role of lipometabolism in gland development and evolution. Additionally, we developed MuskDB (http://muskdb.cn/home/), a freely accessible multi-omics database platform for musk-secreting mammals. <br>The study concludes that the evolution of musk secretion in muskrats and musk deer is likely driven by lipid metabolism and cell specialization. This underscores the complexity of the musk gland and calls for further investigation into musk secretion specific genetic variants.
DOI: 10.5524/102638
title: Supporting data for "High-quality phenotypic and genotypic dataset of barley genebank core-collection to unlock untapped genetic diversity"

description: Genebanks around the globe serve as valuable repositories of genetic diversity, offering not only access to a broad spectrum of plant material but also critical resources for enhancing crop resilience, advancing scientific research, and supporting global food security. To this end, traditional genebanks are evolving into bio-digital resource centres where the integration of phenotypic and genotypic data for accessions can drive more informed decision-making, optimize resource allocation, and unlock new opportunities for plant breeding and research. However, the curation and availability of interoperable phenotypic and genotypic data for genebank accessions is still in its infancy and represents an obstacle to rapid scientific discoveries in this field. Therefore, effectively promoting FAIR, i.e. findable, accessible, interoperable, and reusable, access to these data is vital for maximizing the potential of genebanks and driving progress in agricultural innovation. <br>Here we provide whole genome sequencing data of 812 barley (<i>Hordeum vulgare</i> L.) plant genetic resources (PGRs) and 298 European elite materials released between 1949 and 2021, as well as the phenotypic data for four disease resistance traits and three agronomic traits. The robustness of the investigated traits and the interoperability of genomic and phenotypic data were assessed in the current publication, aiming to make this panel publicly available as a resource for future genetic research in barley. <br>The data showed broad phenotypic variability and high association mapping potential, offering a key resource for identifying genebank donors with untapped genes to advance barley breeding while safeguarding genetic diversity. Here we present the reproducibility code and genotype information. The phenotype data are available from https://doi.org/10.5447/ipk/2024/7.