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905 results for “comparative transcriptomics”
Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism
<p>This dataset is a complement to the following publication: Ahmed M. Abdelmoez, Laura Sardón Puig, Jonathon AB. Smith, Brendan M. Gabriel, Mladen Savikj, Lucile Dollet, Alexander V. Chibalin, Anna Krook, Juleen R. Zierath, and Nicolas J. Pillon. <a href="https://doi.org/10.1152/ajpcell.00540.2019">Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism. </a>Am J Physiol Cell Physiol. 2019 Dec 11.</p> <p>METHODS: Publicly available data from myotubes and skeletal muscle tissues were selected from the GEO database. Raw files were downloaded and robust multi array (RMA) normalization was performed in unison for all samples from the same platform. For each human ENSEMBL, the rat and mouse orthologs were found using the R package BioMart and the arrays were merged based on the human ENSEMBL annotation. The database was then aggregated according to the official human gene symbol. When multiple ENSEMBL were found for a single gene symbol, an average was calculated.</p>
Comparative host transcriptomics as a tool to identify candidate biomarkers for immune reactions in leprosy: A meta-analysis study
<p>The dataset consists of R source code for the individual dataset analysis of the studies and their meta-analysis. It also contains supplementary tables and figure.</p>
The Supplementary Material for the article entitled "Comparative analysis of global transcriptomes in nontyphoidal Salmonella clinical isolates from pediatric patients with and without bacteremia after infecting human intestinal epithelium in vitro"
<p>The Supplementary Material (Additional files 1-5, including Table S1-S4 and Figure S1) for this article.</p> <p> </p> <p><strong>Table S1.</strong> Upregulated genes in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S2.</strong> Downregulated genes in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S3. </strong>The enriched GO terms in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Table S4. </strong>The enriched KEGG pathways in Group B versus Groups A and C+D.</p> <p> </p> <p><strong>Figure S1. </strong>The enriched GO terms and KEGG pathways in Group B relative to Group A. Bar charts show the enriched GO terms (A) and the enriched KEGG pathways (B) by significance power. Color of bars indicate power of significance and length in x axes of bar indicate number of annotated genes in the particular term of pathway. Cnetplots show the relationship between GO term (C) and KEGG pathways (D). Dot size representing GO terms and KEGG pathways indicates number of significantly changed and its annotated genes. The GO terms or KEGG pathways connected through their common and annotated genes. </p>
Fig. 6 in Comparative transcriptome analysis of three Bactrocera dorsalis (Diptera: Tephritidae) organs to identify functional genes in the male accessory glands and ejaculatory duct
Fig. 6. Four examples of the tissue expression profiling of unknown distinct unigenes (>500 bp) expressed highly in male accessory glands and ejaculatory duct tissue of Bactrocera dorsalis. Relative expression levels were determined as described in Fig. 5.
Fig. 4 in Comparative transcriptome analysis of three Bactrocera dorsalis (Diptera: Tephritidae) organs to identify functional genes in the male accessory glands and ejaculatory duct
Fig. 4. Kyoto encyclopedia of gene and genomes (KEGG) analysis of unigenes expressed highly in male accessory glands and ejaculatory duct tissue of Bactrocera dorsalis. Each category contains more than 1 unigene sequences.
Fig. 2 in Comparative transcriptome analysis of three Bactrocera dorsalis (Diptera: Tephritidae) organs to identify functional genes in the male accessory glands and ejaculatory duct
Fig. 2. Clusters of orthologous groups (COG) functional classification of unigenes expressed highly and specifically in male accessory glands and ejaculatory duct tissue of Bactrocera dorsalis.
Fig. 1 in Comparative transcriptome analysis of three Bactrocera dorsalis (Diptera: Tephritidae) organs to identify functional genes in the male accessory glands and ejaculatory duct
Fig. 1. Statistics of sequences expressed specifically in each analyzed tissue of Bactrocera dorsalis.
Fig. 5 in Comparative transcriptome analysis of three Bactrocera dorsalis (Diptera: Tephritidae) organs to identify functional genes in the male accessory glands and ejaculatory duct
Fig. 5. Six examples of the tissue expression profiling of predicted distinct unigenes (>500 bp) expressed highly in male accessory glands and ejaculatory duct tissue of Bactrocera dorsalis. Relative expression levels were determined by qRT-PCR in head (HE), thorax (TH), abdomen (AB), midgut (MG), fat body (FB), Malpighian tubules (MT), testes (TE), and male accessory glands and ejaculatory duct (MAG) samples from B. dorsalis males. Relative expression levels were calculated based on the value in head, which was ascribed an arbitrary value of 1. Different letters above the bars indicate significant differences based on Tukey's test (P ≤ 0.05).
Fig. 3 in Comparative transcriptome analysis of three Bactrocera dorsalis (Diptera: Tephritidae) organs to identify functional genes in the male accessory glands and ejaculatory duct
Fig. 3. Gene ontology (GO) classification of unigenes expressed highly in male accessory glands and ejaculatory duct tissue of Bactrocera dorsalis.
Comparative transcriptomics of tropical woody plants supports fast and furious strategy along the leaf economics spectrum in lianas
<p>Lianas, climbing woody plants, influence the structure and function of tropical forests. Climbing traits have evolved multiple times, including ancestral groups such as gymnosperms and pteridophytes, but the genetic basis of the liana strategy is largely unknown. Here, we use a comparative transcriptomic approach for 47 tropical plant species, including ten lianas of diverse taxonomic origins, to identify genes that are consistently expressed or downregulated only in lianas. Our comparative analysis of full-length transcripts enabled the identification of a core interactomic network common to lianas. Sets of transcripts identified from our analysis reveal features related to functional traits pertinent to leaf economics spectrum in lianas, including upregulation of genes controlling epidermal cuticular properties, cell wall remodeling, carbon concentrating mechanism, cell cycle progression, DNA repair and a large suit of downregulated transcription factors and enzymes involved in ABA-mediated stress response as well as lignin and suberin synthesis. Altogether, these genes are known to be significant in shaping plant morphologies through responses such as gravitropism, phyllotaxy and shade avoidance.</p>
Comparative Analysis of Droplet- vs. Microwell-based Whole Transcriptome Single-Cell Sequencing Technologies in Complex Human Tissues
<p>In the past decade, high-dimensional single-cell omics tools have enabled scientists to study the tumor microenvironment (TME) in unprecedented detail. However, recent investigations suggest that each technique has its unique strengths but also technology-inherent limitations. Here we directly compared two commercially available high-throughput single-cell RNA sequencing (scRNA-seq) technologies - droplet-based 10X Chromium <em>vs.</em> microwell-based BD Rhapsody - using paired samples from patients with localized prostate cancer (PCa) undergoing a radical prostatectomy.</p> <p>Although high technical consistency was observed in unraveling the whole transcriptome, the relative abundance of detectable cell populations differed. This could in part be ascribed to differences in the performance to recover cells with low-mRNA content. Hence, immune cells such as neutrophils are underrepresented in data generated with the widely used droplet-based scRNA-seq protocol, highlighting the importance of considering platform limitations in low mRNA content cell recovery. In contrast, droplet-based scRNA-seq demonstrated superiority in terms of recovering cells of epithelial origin. Moreover, we discovered platform-dependent variabilities in mRNA quantification and cell-type marker annotation, affecting the composition of identified tissue profiles and the exploratory value of the generated datasets. Overall, our study emphasizes the importance of carefully selecting the appropriate scRNA-seq platform to improve cell type representation and obtain a more comprehensive and accurate understanding of the TME.</p>
Comparative transcriptomics of tropical woody plants supports fast and furious strategy along the leaf economics spectrum in lianas
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Data from: Comparative transcriptomics revealed parallel evolution and innovation of photosymbiosis molecular mechanisms in a marine bivalve
<p>Photosymbioses between heterotrophic hosts and autotrophic symbionts are evolutionarily prevalent and ecologically significant. However, molecular mechanisms behind such symbioses remain less elucidated, which hinders our understanding of their origin and adaptive evolution. This study compared gene expression patterns in a photosymbiotic bivalve (<em>Fragum sueziense</em>) and a closely related non-symbiotic species (<em>Trigoniocardia granifera</em>) under different light conditions to detect potential molecular pathways involved in mollusk photosymbiosis. We discovered that the presence of algal symbionts greatly impacted host gene expression in symbiont-containing tissues. We found that the host immune functions were suppressed under normal light compared to those in the dark. In addition, we found that cilia in the symbiont-containing tissues play important roles in symbiont regulation or photoreception. Interestingly, many potential photosymbiosis genes could not be annotated or do not exhibit orthologs in <em>T. granifera</em> transcriptomes, indicating unique molecular functions in photosymbiotic bivalves. Overall, we found both novel and known molecular mechanisms involved in animal-algal photosymbiosis within bivalves. Given that many of the molecular pathways are shared among distantly related host lineages, such as mollusks and cnidarians, it indicates that parallel and/or convergent evolution is instrumental in driving host-symbiont adaptations in diverse organisms.</p>
Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes
<p><span><span><span>Cave-dwelling animals evolve distinct troglomorphic traits, such as loss of eyes, skin pigmentation, and augmentation of senses following long-term adaptation to the perpetual darkness. However, the molecular genetic mechanisms underlying these phenotypic variations remain unclear. In this study, we conducted comparative histology and comparative transcriptomics study of the skin of eight <i>Sinocyclocheilus</i> species (Cypriniformes: Cyprinidae) that included surface and cave-dwelling species. We analyzed four surface and four cavefish species by using next-generation sequencing, and a total of 802,798,907 clean reads were generated and assembled into 505,495,009 transcripts, which contributed to 1,037,334 unigenes. Bioinformatics comparisons of four different surface-cave fish groups revealed between 10,629 and 6442 significantly differentially expressed unigenes. Further, tens of differentially expressed genes (DEGs) potentially related to skin pigmentation were identified. Most of these DEGs (including <i>GNAQ</i>, <i>PKA</i>, <i>NRAS</i>, and <i>p38</i>) are downregulated in cavefish species. They are involved in key signaling pathways of pigment synthesis, such as the melanogenesis, Wnt, and MAPK pathways. This trend of downregulation was confirmed through qPCR experiments. This study will deepen our understanding of the formation of troglomorphic traits in cavefishes.</span></span></span></p>
The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach
<p>The plant genus <em>Oenothera</em> has played an important role in the study of genome evolution and plant defense and reproduction. Here, we built on the 1kp transcriptomic dataset and developed a molecular resource of 63 transcriptomes and present a large-scale comparative study across 29 <em>Oenothera</em> species. We produced 2.3 million transcripts and 25.4 Mb of total length assembly per individual. We used this transcriptome resource to examine genome-wide evolutionary patterns and functional diversification by searching for orthologous genes and performed gene family evolution analysis. We found wide heterogeneity in gene family evolution across the genus, with section <em>Oenothera </em>exhibiting the most pronounced evolutionary changes. Overall, more significant expansions occurred than contractions. We also analyzed the molecular evolution of phenolic metabolism by retrieving proteins annotated for phenolic enzymatic complexes. We identified 1,568 phenolic genes arranged into 83 multigene families that varied widely across the genus. All taxa experienced rapid phenolic evolution involving 33 gene families, which exhibited large expansions, gaining about 2-fold more genes than they lost. Upstream enzymes phenylalanine ammonia-lyase (PAL) and 4-coumaroyl: CoA ligase (4CL) accounted for most of the significant expansions and contractions. Our results suggest that adaptive responses to environmental stress coupled with non-adaptive evolutionary forces have contributed to <em>Oenothera </em>diversification and rapid gene family evolution.</p>
Comparative transcriptomics reveals divergence in pathogen response gene families amongst twenty forest tree species
<p>Forest trees provide critical ecosystem services for humanity that are under threat due to ongoing global change. Measuring and characterizing genetic diversity is key to understanding adaptive potential and developing strategies to mitigate negative consequences arising from climate change. <span>In the area of forest genetic diversity, genetic divergence caused by large-scale changes at the chromosomal level has been largely understudied. In this study, </span>we used the RNA-seq data of twenty co-occurring forest tree species from genera including <em>Acer, Alnus, Amelanchier, Betula, Cornus, Corylus, Dirca, Fraxinus, Ostrya, Populus, Prunus, Quercus, Ribes, Tilia, </em>and<em> Ulmus </em>sampled from Upper Peninsula of Michigan. These data were used to infer the origin and maintenance of gene family variation, species divergence time, as well as gene family expansion and contraction. We identified a signal of common whole genome duplication events shared by core eudicots. We also found rapid evolution, namely fast expansion or fast contraction of gene families, in plant-pathogen interaction genes amongst the studied diploid species. Finally, the results lay the foundation for further research on the genetic diversity and adaptive capacity of forest trees, which will inform forest management and conservation policies.</p>
Comparative transcriptomic analysis reveals coordinated mechanisms of different genotypes of common vetch in response to Al stress
<p><strong>Supplementary Table</strong></p>
Data from: Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects
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Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes
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Data from: Comparative transcriptomics revealed parallel evolution and innovation of photosymbiosis molecular mechanisms in a marine bivalve
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.