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25,372 results for “Transcriptomics”
Data from: Transcriptomic regulation of seasonal coat color change in hares
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High resolution diel transcriptomes of autotetraploid potato reveal expression and sequence conservation among rhythmic genes
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Single-cell spatial transcriptomics of ACAN cKO in WT and 5xFAD mice
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Transcriptome dataset for: The ESCRT protein CHMP5 restricts bone formation by controlling endolysosome-mitochondrion-mediated cell senescence
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The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach
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Spatial transcriptomics of an innate granuloma in a mouse infection model with Chromobacterium violaceum
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Data from: Single-cell transcriptomic analysis of tumor-derived fibroblasts and normal tissue-resident fibroblasts reveals fibroblast heterogeneity in breast cancer
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Transcriptome assemblies associated with: A cnidarian phylogenomic tree fitted with hundreds of 18S leaves
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Protea repens whole transcriptome count data for control and drought treatment for 8 populations, climatic data for the 8 populations and phenotypic data collected, and data used for linear mixed models for climate gene expression/trait correlation testing
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ZipSeq : barcoding for real-time mapping of single cell transcriptomes
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DATA for manuscript entitled "Integrating Transcriptomes and Somatic Mutations to Identify RNA Methylation Regulators as a Prognostic Marker in Hepatocellular Carcinomas"
<p><strong>Raw data of TCGA dataset and 7-meta data.</strong></p>
Transcriptome-based target-enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)
<p>Bait sets, sequences, trees and scripts</p>
Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data
<p>This repository contains input files from the synthetic, curated, and processed experimental single-cell gene expression datasets used in BEELINE.</p> <p>New in version 3:<br> 1) Ground-truth networks used for analysis of experimental scRNA-seq datasets for mouse and human datasets<br> 2) Changed license to CC BY-NC 4.0 from GPL v3.0 to account for the non-commercial clause for the network data</p>
Data from: Transcriptome analysis reveals nutrition‐ and age‐related patterns of gene expression in the fat body of pre‐overwintering bumble bee queens
<p>Many diapausing insects undergo a nutrient storage period prior to their entry into diapause. Bumble bee queens diapause as adults in the winter preceding their spring nest initiation period. Before diapause, they sequester glycogen and lipids, which they metabolize during the overwintering period. We used RNA sequencing to examine how age and nectar diet (specifically, the concentration of sucrose in nectar) impact gene expression in the pre-overwintering bumble bee queen fat body, the "liver-like" organ in insects with broad functions related to nutrient storage and metabolism. We found that diet on its own, and in combination with age, impacts the expression of genes involved in detoxification. Age was also a strong driver of gene expression, especially at earlier ages (up to 3 days). In addition to these molecular correlates of diet and age, we also found a putative molecular signature of diapause entry or preparation in adult queens in the oldest age group (12 days) fed the most sucrose-rich diet, based on comparisons between our data set and another transcriptome data set from bumble bee queens. This transcriptomic pattern suggests that preparation for (or entry into) diapause might be in part mediated by nutritional state in bumble bee queens. Collectively, these findings show that there are molecular processes in the fat body that are responsive to sucrose levels in the diet and/or associated with age-related maturational changes. A better understanding of these processes may shed light on important aspects of bumble bee biology, such as queen responses to nutritional and other forms of stress, and the factors that regulate their entrance into diapause.</p>
Comparative transcriptomics of the venoms of continental and insular radiations of West African cones
<p>The transcriptomes of the venom glands of 13 closely related species of vermivorous cones endemic to West Africa from genera <i>Africonus</i> and <i>Varioconus</i> were sequenced and venom repertoires compared within a phylogenetic framework. The total number of conotoxin precursors per species varied between 108 and 221. Individuals of the same species shared about one fourth of the total conotoxin precursors. The number of common sequences was drastically reduced in the pairwise comparisons between closely related species and the phylogenetical signal was totally eroded at the genus level (no sequence was identified as shared-derived), due to the intrinsic high variability of these secreted peptides. A common set of four conotoxin precursor superfamilies (T, O1, O2, and M) was expanded in all studied cone species, and thus, they are considered the basic venom toolkit for hunting and defense in the West African vermivorous cone snails. Maximum likelihood ancestral character reconstructions inferred shared conotoxin precursors preferentially at internal nodes close to the tips of the phylogeny (between individuals and between closely related species) as well as in the common ancestor of <i>Varioconus</i>. Besides the common toolkit, the two genera showed significantly distinct catalogues of conotoxin precursors in terms of type of superfamilies present and the abundance of members per superfamily, but had similar relative expression levels indicating functional convergence. Differential expression comparisons between vermivorous and piscivorous cones highlighted the importance of the A and S superfamilies for fish hunting and defense.</p>
Data from: Profiling extracellular long RNA transcriptome in human plasma and extracellular vesicles for biomarker discovery
<p>The recent discovery of extracellular RNAs in blood, including RNAs in extracellular vesicles (EVs), combined with low-input RNA-sequencing advances have enabled scientists to investigate their role in human disease. To date, most studies have been focusing on small RNAs, and methodologies to optimize long RNAs measurement are lacking. We used plasma RNA to assess the performance of six long RNA sequencing methods, at two different sites, and we report their differences in reads (%) mapped to the genome/transcriptome, number of genes detected, long RNA transcript diversity, and reproducibility. Using the best performing method, we further compare the profile of long RNAs in the EV- and no-EV-enriched RNA plasma compartments. These results provide insights on the performance and reproducibility of commercially available kits in assessing the landscape of long RNAs in human plasma and different extracellular RNA carriers that may be exploited for biomarker discovery.</p>
Single-cell Transcriptomic Analysis Identifies Extensive Heterogeneity in the Cellular Composition of Mouse Achilles Tendons
<p>Tendon is a dense connective tissue that stores and transmits forces between muscles and bones. Cellular heterogeneity is increasingly recognized as an important factor in the biological basis of tissue homeostasis and disease, yet little is known about the diversity of cell types that populate tendon. To address this, we determined the heterogeneity of cell populations within mouse Achilles tendons using single-cell RNA sequencing. In assembling a transcriptomic atlas of Achilles tendons, we identified 11 distinct types of cells, including 3 previously undescribed populations of tendon fibroblasts. This table contains differential gene expression for specific genes identified in distinct populations of cells within tendon tissue. </p>
Data from: Transcriptome sequencing reveals signatures of positive selection in the spot-tailed earless lizard
<p><span><span><span><span><span><span><span><span><span><span><span>The continual loss of threatened biodiversity is occurring at an accelerated pace. High-throughput sequencing technologies are now providing opportunities to address this issue by aiding in the generation of molecular data for many understudied species of high conservation interest. Our overall goal of this study was to begin building the genomic resources to continue investigations and conservation of the Spot-Tailed Earless lizard. Here we leverage the power of high-throughput sequencing to generate the liver transcriptome for the Northern Spot-Tailed Earless Lizard (<i>Holbrookia lacerata</i>)<i> </i>and Southern Spot-Tailed Earless Lizard (<i>Holbrookia</i> <i>subcaudalis</i>), which have declined in abundance in the past decades, and their sister species, the Common Lesser Earless Lizard (<i>Holbrookia maculata</i>). Our efforts produced high quality and robust transcriptome assemblies validated by <b>1</b>) quantifying the number of processed reads represented in the transcriptome assembly and <b>2</b>) quantifying the number of highly conserved single-copy orthologs that are present in our transcript set using the BUSCO pipeline. We found 1,361 1-to-1 orthologs among the three <i>Holbrookia </i>species, <i>Anolis carolinensis</i>, and <i>Sceloporus undulatus</i>. We carried out dN/dS selection tests using a branch-sites model and identified a dozen genes that experienced positive selection in the <i>Holbrookia</i> lineage with functions in development, immunity, and metabolism. Our single-copy orthologous sequences additionally revealed significant pairwise sequence divergence (~.73%) between the Northern <i>H. lacerata</i> and Southern <i>H.</i> <i>subcaudalis </i>that further supports the recent elevation of the Southern Spot-Tailed Earless Lizard to full species<i>.</i></span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Division of functional roles for termite gut protists revealed by single-cell transcriptomes
<p>The microbiome in the hindgut of wood-feeding termites comprises various species of bacteria, archaea, and protists. This gut community is indispensable for the termite, which thrives solely on recalcitrant and nitrogen-poor wood. However, the difficulty in culturing these microorganisms has hindered our understanding of the function of each species in the gut. Although protists predominate in the termite gut microbiome and play a major role in wood digestion, very few culture-independent studies have explored the contribution of each species to digestion. Here, we report single-cell transcriptomes of four protists species comprising the protist population in worldwide pest <em>Coptotermes formosanus</em>. Comparative transcriptomic analysis revealed that the expression patterns of the genes involved in wood digestion were different among species, reinforcing their division of roles in wood degradation. Transcriptomes, together with enzyme assays, also suggested that one of the protists, <em>Cononympha leidyi</em>, actively degrades chitin and assimilates it into amino acids. We propose that C. leidyi contributes to nitrogen recycling and inhibiting infection from entomopathogenic fungi through chitin degradation. Two of the genes for chitin degradation were further revealed to be acquired via lateral gene transfer (LGT) implying the importance of LGT in the evolution of symbiosis. Our single-cell-based approach successfully characterized the function of each protist in termite hindgut and explained why the gut community includes multiple species.</p>
Draft transcriptome assembly of Aipysurus laevis
<p><em>De novo</em> Trinity transcriptome assembly from six <em>Aipysurus laevis</em> tissues from multiple individuals. This data is complementary to DOI:10.5281/zenodo.3975254.</p>
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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.