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25,372 results for “Transcriptomics”
Spatial reconstruction of the early hepatic transcriptomic landscape after an acetaminophen overdose using single-cell RNA sequencing
<p>We leveraged single-cell RNA sequencing to understand the early molecular events that define the hepatocyte response to acetaminophen exposure at a subpopulation level. We spatially assigned hepatocytes along the portol-central vein axis by using established landmark genes. By spatially assigning the hepatocytes were were able to account for innate differences in gene expression that existed along this gradient. The excel files herein provide the full list of differentially expressed genes between key subpopulations of interest. Additionally, we classified genes as either pericentral zonated, periportal zonated, or non-zonated, the full list of genes and their spatial assignments are included in the appropriate excel file. </p>
Transcriptomics Reveal Specific Molecular Mechanisms Underlying Transgenerational Immunity in Manduca sexta
<p class="FirstParagraph">The traditional view of innate immunity in insects is that every exposure to a pathogen triggers an identical and appropriate immune response, and that prior exposures to pathogens do not confer any protective (i.e. adaptive) effect against subsequent exposure to the same pathogen. This view has been challenged by experiments demonstrating that encounters with sub-lethal doses of a pathogen can prime the insect's immune system and thus, have protective effects against future lethal doses. Immune priming has been reported across several insect species, including the red flour beetle, the honeycomb moth, the bumblebee, and the European honeybee, among others. Immune priming can also be trans-generational where the parent's pathogenic history influences the immune response of its offspring. Phenotypic evidence of transgenerational immune priming (TGIP) exists in the tobacco moth <i>Manduca sexta</i> where first instar progeny of mothers injected with the bacterium <i>Serratia marcescens</i> exhibited a significant increase of <i>in-vivo</i> bacterial clearance. To identify the gene expression changes underlying TGIP in <i>Manduca sexta</i>, we performed transcriptome-wide, trans-generational differential gene expression analysis on mothers and their offspring after mothers were exposed to <i>S. marcescens</i>. We are the first to perform transcriptome-wide analysis of the gene expression changes associated with TGIP in this ecologically relevant model organism. We show that maternal exposure to both heat-killed and live <i>S. marcescens</i> has strong and significant trans-generational impacts on gene expression patterns in their offspring, including up-regulation of peptidoglycan recognition protein, toll-like receptor 9, and the antimicrobial peptide cecropin.</p>
Single-nucleus Transcriptomics of IDH1- and TP53-mutant Glioma Stem Cells Displays Diversified Commitment on Highly Invasive Cancer Progenitors
<p><strong>Fig. S1</strong>. <strong>Marker genes for Seurat clusters.</strong> (<strong>A</strong>) distribution of marker genes for cluster 0 on the 2D-UMAP space. (<strong>B</strong>) distribution of marker genes for cluster 1 on the 2D-UMAP space. (<strong>C</strong>) distribution of marker genes for cluster 2 on the 2D-UMAP space. (<strong>D</strong>) distribution of marker genes for cluster 3 on the 2D-UMAP space. (<strong>E</strong>) distribution of marker genes for cluster 4 on the 2D-UMAP space. (<strong>F</strong>) distribution of marker genes for cluster 5 on the 2D-UMAP space. (<strong>G</strong>) Stuck violin plot of marker gene expression for Seurat clusters (bottom panel) and their annotation (right side panel). The violin shape displays the number of the cells expressing a gene, the continuous color panel defines median expression value of a gene from the absence of expression (white) to high expression (dark blue).</p> <p><strong>Fig. S2</strong>. <strong>Expression of genes marking cell malignization.</strong> (<strong>A</strong>) expression of collagens in Surat clusters (bottom panel) (<strong>B</strong>) expression of genes linked to Migration and ECM in Surat clusters (bottom panel) (<strong>C</strong>) expression of genes classified as Proto-oncogenes in Surat clusters (bottom panel). The violin shape displays the number of the cells expressing a gene, the violin color defines the Seurat cluster. Gene expression displayed in log-transformed normalized expression values.</p> <p><strong>Fig. S3</strong>. <strong>Expression of genes involved in proliferation and survival of cancer cells.</strong> (<strong>A</strong>) Genes involved in Wnt-pathway in Surat clusters (bottom panel). (<strong>B</strong>) Genes involved in Akt-pathway in Surat clusters (bottom panel). (<strong>C</strong>) Genes inducing resistance to cancer therapeutics in Surat clusters (bottom panel). The violin shape displays the number of the cells expressing a gene, the violin color defines the Seurat cluster. Gene expression displayed in log-transformed normalized expression values.\</p> <p><strong>Fig. S4</strong>. <strong>Expression of genes marking CSC profile.</strong> (<strong>A</strong>) Ion channel genes in Surat clusters (bottom panel). (<strong>B</strong>) Antioncogenes in Surat clusters (bottom panel). <strong>C</strong>. Stem-cell genes in Surat clusters (bottom panel). (<strong>D</strong>) Antiapoptotic genes in Surat clusters (bottom panel). The violin shape displays the number of the cells expressing a gene, the violin color defines the Seurat cluster. Gene expression displayed in log-transformed normalized expression values.</p> <p><strong>Fig. S5</strong>. <strong>Genes differentially expressed between UMAP clusters</strong>. (<strong>A</strong>) Heatmap for wt-GSCs. (<strong>B</strong>) Heatmap for mt-GSCs. Upper colour panel in the heatmap designates Seurat clusters. Gene expression is indicated by continuous colour panel starting from the most downregulated (blue) to the most upregulated (red).</p> <p><strong>Fig. S6</strong>. <strong>Marker genes defying cell annotations</strong>. (<strong>A</strong>) Stack violin plot displays marker gene expression in wt-GSC clusters. (<strong>B</strong>) Stack violin plot displays marker gene expression in mt-GSC clusters. Genes grouped by cell annotations (side description) and UMAP clusters (down column bar). The violin shape displays the number of the cells expressing a gene, the continuous color panel defines median expression value of a gene from the absence of expression (white) to high expression (dark blue).</p> <p><strong>Fig. S7</strong>. <strong>Differentially expressed proliferation and adhesion pathways comparing mutant samples to wild type.</strong> (<strong>A</strong>) ERBB signalling pathway. (<strong>B</strong>) Wnt signalling pathway. (<strong>C</strong>) Genes linked to Focal adhesion. (<strong>D</strong>) Genes classified as Cell adhesion molecules. Red rectangles display upregulated genes (proteins), green rectangles define downregulated genes (proteins). Pictures obtained by KEGG pathview.</p> <p><strong>Table S1. Glioma genotyping primers</strong></p> <p><strong>Table S2. Smart-seq2 Primers</strong></p>
Parasitic cnidarians (Myxozoa) do not retain key oxygen-sensing and homeostasis tool-kit genes: Transcriptome assemblies
<p>For aerobic organisms, both the Hypoxia-Inducible Factor (HIF) pathway and the mitochondrial genomes are key players in regulating oxygen homeostasis. However, recent work has suggested that these mechanisms are not as highly conserved as previously thought, prompting more thorough surveys across animal higher taxonomic levels, which would in turn permit testing of hypotheses about the ecological conditions that may have facilitated evolutionary loss of such genes. The phylum Cnidaria is known to harbor wide variation in mitochondrial genome morphology, from typical single circular chromosomes to fragmented linear chromosomes. More recently, members of the cnidarian clade Myxozoa, comprising obligate endoparasites, were shown to have lost their mitochondrial genome, suggesting that variation in environmental oxygen availability may be a key determinant in the evolution of metabolic gene networks. Here, we surveyed genomes and transcriptomes across 42 cnidarian species for the presence of HIF pathway members (HIFa, EGLN, VHL), as well as for an assortment of hypoxia, mitochondrial, and stress-response toolkit genes. We find that presence of the HIF pathway, as well as number of genes associated with mitochondria, hypoxia, and stress response, do not vary based on mitochondrial genome morphology. More interestingly, we uncover evidence that myxozoans have lost the canonical HIF pathway repression machinery, potentially altering HIF pathway functionality to work under the specific conditions of their parasitic lifestyles. In addition, relative to other cnidarians, myxozoans show loss of large proportions of genes associated with the mitochondrion (~39%), and involved in response to hypoxia (~27.5%) and general stress (~32%). Our results provide additional evidence that the HIF regulatory machinery is evolutionarily labile and that variations in the canonical system have evolved in many animal groups.</p>
Transcriptomic analysis demonstrates the expression, origin and function of lncRNAs in multiple skin diseases
<p>Transcriptomic analysis demonstrates the expression, origin and function of lncRNAs in multiple skin diseases</p>
Elemental bioimaging and transcriptomics – no evidence of altered gene expression after single injection of Gadolinium-based contrast agents in mice cerebellum
<p>single read RNA data for GBCA study</p>
Spatially resolved transcriptomics reveals innervation-responsive functional clusters in skeletal muscle
<p>Spatial Transcriptomics Data of murine skeletal muscle undergoing reversible nerve injury. Accompanying the manuscript, D'Ercole et al. <strong>"Spatially resolved transcriptomics reveals innervation-responsive functional clusters in skeletal muscle".</strong></p> <p> </p> <p><strong>Release v1: </strong>This release Includes all the code used to generate the figures and the processed and integrated original dataset in rds format.</p> <p> </p>
Supplementary Data - Transcriptomic Profiling Does Not Refine Mastocytosis Diagnosis
<p>Supplementary data including cohort characterisctics, read counts (CPM), differential expression outputs, correlation analysis outputs and more specific analysis of the dataset described in the paper "Transcriptomic Profiling Does Not Refine Mastocytosis Diagnosis".</p> <p> </p> <p>Abstract:</p> <p>The recent 5th edition of the WHO update on hematopoietic cancers includes relevant changes to the diagnostic criteria of Mastocytosis. Yet, it remains entirely unclear whether transcriptional profiles of bone marrow of patients with Mastocytosis instruct diagnostic, prognostic or predictive information as it has been shown in many other cancer types. Here we show that transcriptional profiling of a large and clinically well-annotated dataset of Systemic Mastocytosis (SM) patients fails to achieve a further diagnostic refinement of SM above the level of genomic and clinical parameters. Yet, transcriptional differences between clinical and genomic SM subgroups robustly link the expression of certain genes to the MARS score as a surrogate of prognosis.</p>
Paired blood-brain transcriptomes (GTEx v8), age and sex preserved
<p>This dataset includes pre-normalized paired blood-brain RNA-sequencing profiles from donors included in the Genotype Tissue Expression (GTEx) Project (v8). Variances in gene expression associated with age and sex were preserved during normalization. These data are formatted for BrainGENIE. </p>
HypoRiPPAtlas - plant transcriptome datasets
<p>Plant transcriptome datasets from Supplementary Table S2</p>
Phylogenomic data of Camellia section Paracamellia based on transcriptomes and plastomes
<p><em>Camellia</em> section <em>Paracamellia</em> of the genus <em>Camellia</em> (Theaceae) includes major woody oil crops in China and relative wild species as valuable genetic resources for breeding. However, the phylogeny and origin of <em>C. oleifera</em> and its relative species are still uncertain. In this study, the transcriptomes of 22 samples and plastomes of 19 samples were sequenced and assembled. Finally, the dataset of phylogenomic matrices was generated, including 982 and 326 single-copy orthologous (SCO) genes generated from transcriptomes data and the plastid matrix used for phylogenetic analysis. Please cite this article as doi: 10.1111/jse.12948.</p>
Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation
<p>Raw microscopy images underlying the publication "Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation"</p>
Long-read transcriptome data (Iso-Seq) of the human and mouse brain
<p>Datasets from "<strong>Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing</strong>", SK.Leung, A.Jeffries. et al. (2021)</p> <p>Deposited files are generated from running Cupcake, SQANTI2 (v7.4) and filter. <br> Note, only the files generated from SQANTI2 filtering are deposited. <br> To re-run SQANTI, use the files in cupcake_collapse folder as input. </p> <p>Please refer to code (https://github.com/SziKayLeung/Whole_Transcriptome_Paper) for more information. </p> <p>Datasets: <br> - AdultCTX: Adult human prefrontal cortex tissue (n = 4) merged dataset<br> - FetalCTX: Fetal human prefrontal cortex tissue (n = 3) merged dataset<br> - FetalHIP: Fetal human hippocampus tissue (n = 2, subset of FetalCTX) merged dataset<br> - FetalSTR: Fetal human striatum tissue (n = 2, subset of FetalCTX) merged dataset<br> - MouseCTX: Mouse entorhinal cortex tissue (n = 12) merged dataset</p>
Single-cell and spatial transcriptomics of cardiac neural crest reveal a dual role of vinculin in Tgf beta signaling and cell-extracellular matrix interaction during cardiac outflow tract development
<p>single-cell RNA-seq data analysis:</p> <p>all.cncc.combined.EMBO.mapped.Rdata: public CNCC single-cell RNA-seq data integration</p> <p>E13.5_CNCC_merged_updated.Rdata: single-cell RNA-seq data of E13.5 CNCC generated in Elly lab</p> <p>all.seurat.GFP.Rdata: scRNA-seq data with GFP detected</p> <p>visium.merge_AB.control.Rdata: R processed ST data for slice A and B</p> <p>visium.merge_CD.mutant.Rdata: R processed ST data for slice A and B</p> <p> </p>
Ganglioglioma deep transcriptomics reveals primitive neuroectoderm neural precursor-like population
<p>Ganglioglioma tumor single nucleus RNA sequencing, cellular indexing of transcriptomes by sequencing, and spatial transcriptomics data sets to accompany manuscript of the same title posted to BioRxiv. </p>
Perfluorooctanoic acid induces transcriptomic alterations in 2nd trimester human cytotrophoblasts
<p>Poly- and perfluroroalkylated substances (PFAS) are a major class of surfactants used in industry applications and consumer products. Despite efforts to reduce the usage of PFAS due to their environmental persistence, compounds such as perfluorooctanoic acid (PFOA) are widely detected in human blood and tissue. While growing evidence supports that prenatal exposures to PFOA and other PFAS are linked to adverse pregnancy outcomes, the target organs and pathways remain unclear. Recent investigations in mouse and human cell lines suggest that PFAS may impact the placenta and impair trophoblast function. In this study, we investigated the effects of PFOA on cytotoxicity and the transcriptome in cultured 2nd-trimester human CTBs. We show that PFOA significantly reduces viability and induces cell death at 24h, in a concentration-dependent manner. At subcytotoxic concentrations, PFOA impacted expression of hundreds of genes, including several molecules (CRH, IFIT1, and TNFSF10) linked with lipid metabolism and innate immune response pathways. Furthermore, in silico analyses suggested that regulatory factors such as peroxisome proliferator-activated receptor (PPAR)-mediated pathways may be especially important in response to PFOA. In summary, this study provides evidence that PFOA alters primary human CTB viability and gene pathways that could contribute to placental dysfunction and disease.</p>
Datasets used in Consensus Clustering Problem in Single-cell Transcriptome Data Analysis
<p>20 benchmark scRNA-seq datasets used in Consensus Clustering Problem in Single-cell Transcriptome Data Analysis. In every datasets .zip files, it provided raw data files, the processed R code and the corresponding R objects. The datasets.xlsx file provided the detailed information of 20 datasets.</p>
Proteomic and transcriptomic analyses to decipher the chitinolytic response of Jeongeupia spp.
<p>Raw data sets of the research article "Proteomic and transcriptomic analyses to decipher the chitinolytic response of Jeongeupia spp." in MarineDrugs, 2023. Including evaluation files of the MS/MS spectrometric data on the intracellular proteomics & transcriptomics, as well as the secretome. Furthermore includes signal peptide prediction data, dbCAN3.0 carbohydrate-active enzyme prediction, eggNOG-Mapper functional annotations and gene IDs of the unique upregulated/secreted enzymes and upregulated transcripts.</p>
Data from: A step in the deep evolution of Alvinellidae (Annelida: Polychaeta): A phylogenomic comparative approach based on transcriptomes
<p>Alvinellid worms are a family of endemic and closely related species from deep-sea hydrothermal vents in the Pacific and Indian Oceans. These annelid worms, sister group to the Ampharetidae, occupy a wide range of ecological niches, some of which include the most thermotolerant marine animals described to date such as the Pompeii worm <em>Alvinella pompejana</em>, and other species living at much lower temperatures such as<em> Paralvinella grasslei </em>or <em>Paralvinella pandorae</em>. The phylogeny of this family has not yet been studied extensively. It is, however, a complex case with conflicting molecular phylogenies, the main question being the monophyletic or polyphyletic character of the genus Paralvinella. We carried out a comprehensive study of the phylogeny of this family using the best molecular data currently available from RNAseq datasets. The study is based on the assembly of several hundred transcripts for 11 of the 14 species described or in description. The results obtained by the most popular phylogenetic inference models (gene concatenation and maximum likelihood, or coalescent-based methods from gene trees) are compared, and an attempt is made to use sequence insertion and deletion information to evaluate and strengthen our choice over the different phylogenies using a newly-developed maximum likelihood method. Although our study does not allow to definitively assert the phylogeny of the Alvinellidae (three species are still missing), we propose to support the initial hypothesis of the monophyly of the Paralvinella proposed by Desbruy`eres and Laubier on the basis of the morphology of the species, in which the species Paralvinella pandorae and Paralvinella unidentata are basal in the genus Paralvinella and grouped together within the subgenus nautalvinella. Following a clock calibration, the radiation of the Alvinellidae, dated between 55 and 78 Myr, took place very rapidly, resulting in high rates of incomplete lineage sorting between the first ancestors and probable gene transfers between the Alvinella, Nautalvinella and the rest of the Paralvinella lineages.</p>
Single-Cell Transcriptomics Reveals Pre-existing COVID-19 Vulnerability Factors in Lung Cancer Patients
<p>This dataset contains the processed scRNA-seq data and code used to investigate the association between lung cancers and COVID-19. Please refer to the article 'Single-Cell Transcriptomics Reveals Pre-existing COVID-19 Vulnerability Factors in Lung Cancer Patients' for the detailed data and method description.</p> <p>covid_cancer.rds: the processed scRNA-seq data saved as a Seurat object.</p> <p>notebooks.zip: Jupyter notebooks containing code for data analysis.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.