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25,372 results for “Transcriptomics”
Different DNA methylome, transcriptome and histological features in uterine fibroids with and without MED12 mutations
<p><span><span><span><span>Somatic mutations in Mediator complex subunit 12 (MED12m) have been reported as a biomarker of uterine fibroids (UFs). However, the role of MED12m is still unclear in the pathogenesis of UFs. Therefore, we investigated the differences in DNA methylome, transcriptome, and histological features between MED12m-positive and -negative UFs. </span></span></span></span><span><span><span><span>DNA methylomes and transcriptomes were obtained from MED12m-positive and -negative UFs and myometrium, and hierarchically clustered. Differentially expressed genes in comparison with the myometrium and co-expressed genes detected by weighted gene co-expression network analysis were subjected to gene ontology enrichment analyses. The amounts of collagen fibers and the number of blood vessels and smooth muscle cells were histologically evaluated. </span></span></span></span><span><span><span><span>Hierarchical clustering based on DNA methylation clearly separated the myometrium, MED12m-positive, and MED12m-negative UFs. MED12m-positive UFs showed the increased activities of extracellular matrix formation, whereas MED12m-negative UFs had the increased angiogenic activities and smooth muscle cell proliferation. </span></span></span></span><span><span><span><span>The MED12m-positive and -negative UFs had different DNA methylation, gene expression, and histological features.</span></span></span></span> <span><span><span><span>The MED12m-positive UFs form the tumor with a rich extracellular matrix and poor blood vessels and smooth muscle cells compared to the MED12m-negative UFs, suggesting MED12 mutations affect the tissue composition of UFs.</span></span></span></span></p>
Supplementary data for Orciraptor agilis de novo transcriptome assembly study
<p>Supplementary Data for study "Comparative transcriptomics reveals the molecular toolkit used by an algivorous protist for cell wall perforation"</p>
Hexagenia limbata early instar transcriptome assemblies & annotation
<p>This data is part of a publication in process ("Characterizing Hox genes in mayflies (Ephemeroptera), with <em>Hexagenia limbata</em> as a new mayfly model"). The CLC contig data and original read sequencing methodology is also described in the masters thesis of coauthor Christopher Gonzalez (thesis title: "Evolutionary Developmental Biology in the Mayfly Hexagenia limbata, with a Focus on Hox Genes.")</p> <p><strong>H_limbata_CLC_contigs.fa, H_limbata_ORP_contigs.fa</strong></p> <p>The two contig assemblies were assembled from the same set of transcriptome reads (NCBI SRA accession SRX6489924), which were sequenced from a pooled sample of approximately 100 μl of whole-body nymphs, most 1st instar and some 2nd instar. The transcriptomes differ in their assembly methods, with CLC referring to assembly within CLC Genomics WorkBench v.6.0.4 (CLCBio, Boston, MA), while ORP refers to contig assembly via the Oyster River Protocol v2.2.6 (MacManes, 2018).</p> <p><strong>Hexagenia_ORP_peps.fa</strong></p> <p>Peptide sequences generated via TransDecoder v5.5.0 (https://github.com/TransDecoder/TransDecoder/wiki) from the ORP assembly were used to assess the phylogeny of Hox genes in H. limbata. Note that the generated header names do not match those of the contig or annotation files. </p> <p><strong>H_limbata_ORP_annotation.tsv</strong></p> <p>Protein homology annotations for the ORP assembly were done via Diamond v0.9.24.125 (Buchfink et. al., 2015). All headers refer to the generated contig names in H_limbata_ORP_contigs.fa.</p> <p> </p>
Inferring causal cell-cell communication from single-cell transcriptomics
<p>Data used to produce the analysis in "Inferring causal cell-cell communication from single-cell transcriptomics" by Almet and Nie (2022)</p>
Integrated single cell transcriptomics of cerebrospinal fluid cells in early Multiple Sclerosis
<p>h5ad file for "Integrated single cell transcriptomics of cerebrospinal fluid cells in early Multiple Sclerosis"</p>
Pre-fitted Bayesian models for "Gene panel selection for targeted spatial transcriptomics"
<p>simulation_parameters_DARTFISH_slim.rds: Bayesian model fitted on the Zhang dataset.</p> <p>simulation_parameters_MERFISH_slim.rds: Bayesian model fitted on the Moffit dataset.</p> <p>simulation_parameters_osmFISH_slim.rds: Bayesian model fitted on the Codeluppi dataset.</p> <p> </p>
The transcriptomic landscape of normal and ineffective erythropoiesis at single cell resolution
<p><span>Ineffective erythropoiesis, the death of maturing erythroid cells, is a common cause of anemia. To better understand why this occurs, we studied the fates and adaptations of single erythroid marrow cells from individuals with Diamond Blackfan anemia (DBA), del(5q) myelodysplastic syndrome (del(5q) MDS), and normal controls, and defined an unhealthy (vs. healthy) differentiation trajectory, using velocity pseudotime and cell surface protein assessment. The pseudotime trajectories diverge immediately after the cells upregulate transferrin receptor (CD71), import iron, and initiate heme synthesis, although cell death occurs much later. Cells destined to die highly express heme-responsive genes, including ribosomal protein and globin genes. In contrast, surviving cells downregulate heme synthesis, while upregulating DNA damage response, hypoxia, and HIF1 pathways. Surprisingly, 24±12% of cells from controls follow the unhealthy trajectory, implying that heme also regulates cell fate decisions during normal red cell production. Del(5q) MDS (unlike DBA) results from somatic mutations, so many normal (unmutated) erythroid cells persist. By independently tracking their trajectory, we gained insight into why they cannot expand to prevent anemia. In addition, we show that intron retention is especially prominent during red cell differentiation. The additional information provided by messages with retained introns also allowed us to align data from multiple independent experiments and thus accurately query the transcriptomic changes that occur as single erythroid cells mature. </span></p>
The transcriptome responses of Fusarium head blight and Fusarium root rot in B. distachyon
<p><em>Fusarium graminearum</em> causes Fusarium head blight (FHB) and Fusarium root rot (FRR) in small-grain cereals. The host response to FRR and the transcriptome responses differences of FHB and FRR are not well studied. Using the model <em>Brachypodium</em> <em>distachyon</em> (Bd), the RNA-seq transcriptome response of Bd to <em>F</em>. <em>graminearum</em> (Fg) infection of heads and roots was carried out. Additionally, the RNA-seq transcriptome response and predicted secretome within the same infected material were performed against in vitro samples of Fg.</p>
Timing of blood sample processing affects the transcriptomic and epigenomic profiles in CD4+ T-cells of atopic subjects
<p><span>Optimal</span><span> pre-analytical conditions for blood sample processing and isolation of selected cell populations for subsequent transcriptomic and epigenomic studies are required to obtain robust and reproducible results. This pilot study was conducted to investigate the potential effects of timing of CD4<sup>+</sup> T-cell processing from peripheral blood of atopic and non-atopic adults on their transcriptomic and epigenetic profiles. Two heparinized blood samples were drawn from each of three atopic and three healthy individuals. For each individual, </span><span>CD4<sup>+</sup></span><span> T-cells were isolated from the first blood sample within 2 hours (immediate) or from the second blood sample after 24 hours storage (delayed). RNA sequencing (RNA-Seq) and histone H3K27 acetylation chromatin immunoprecipitation sequencing (ChIP-Seq) analyses were performed. A multiplicity of genes was shown to be differentially expressed in immediately processed </span><span>CD4<sup>+</sup></span><span> T-cells from atopic versus healthy subjects. These differences disappeared when comparing delayed processed cells due to a drastic change in expression levels of atopy-related genes in delayed processed </span><span>CD4<sup>+</sup></span><span> T-cells from atopic donors. This finding was further validated on the epigenomic level by examining H3K27 acetylation profiles. In contrast, transcriptomic and epigenomic profiles of blood </span><span>CD4<sup>+</sup></span><span> T-cells of healthy donors remained rather unaffected. Taken together, for successful transcriptomics and epigenomics studies, detailed standard operating procedures developed on the basis of samples from both healthy and disease conditions are implicitly recommended.</span></p>
Fig. 3 in Deep Instability in the Phylogenetic Backbone of Heteroptera is Only Partly Overcome by Transcriptome-Based Phylogenomics
Fig. 3. Metrics resulting from quartet sampling of the amino acid alignment over the phylogeny resulting from maximum likelihood analyses of amino acids. Clade support is depicted as: QC/QD/QI.
Fig. 1 in Deep Instability in the Phylogenetic Backbone of Heteroptera is Only Partly Overcome by Transcriptome-Based Phylogenomics
Fig. 1. Phylogeny of Heteroptera resulting from partitioned analysis of concatenated nucleotides. Clade support is based on bootstrap replicates and the scale bar is average substitutions per site.
Fig. 2 in Deep Instability in the Phylogenetic Backbone of Heteroptera is Only Partly Overcome by Transcriptome-Based Phylogenomics
Fig. 2. Metrics resulting from quartet sampling of the nucleotide alignment over the phylogeny resulting from maximum likelihood analyses of concatenated nucleotides. Clade support is depicted as: QC/QD/QI.
Fig. 4 in Deep Instability in the Phylogenetic Backbone of Heteroptera is Only Partly Overcome by Transcriptome-Based Phylogenomics
Fig. 4. Subtree of Pentatomomorpha based on the ML analysis of concatenated nucleotides and subsequent quartet sampling. Clade support is depicted as: QC/QD/QI.
Transcriptomic cross-species analysis of chronic liver disease reveals consistent regulation between humans and mice
<p>Data used to analyse chronic and acute liver disease in mice and human as described in <a href="https://doi.org/10.1002/hep4.1797">Holland et al. 2021</a>.</p> <p>Corresponding code is available on <a href="https://github.com/saezlab/liver-disease-atlas">GitHub</a>.</p>
Supplementary material 1 from: Graupner N, Boenigk J, Bock C, Jensen M, Marks S, Rahmann S, Beisser D (2017) Functional and phylogenetic analysis of the core transcriptome of Ochromonadales. Metabarcoding and Metagenomics 1: e19862. https://doi.org/10.3897/mbmg.1.19862
KEGG orthologous genes of the core trancriptome of the herein investigated Ochromonadales (Poteriospumella lacustris strains JBC07, JBM10, JBNZ41; Poterioochromonas malhamensis DS; Spumella vulgaris 199hm; Pedospumella encystans JBMS11) used for phylogenetic analyses.
The salivary gland transcriptome of Varroa destructor reveals suitable targets for RNAi-based mite control
<p><span>The mite <em>Varroa destructor</em> has a dramatic impact on beekeeping, and is one of the main causes of honey bee colony losses. This ectoparasite feeds on honey bees’ liquid tissues through a wound created on the host integument, which determines weight loss, a reduced lifespan and the transmission of viral pathogens. However, despite its importance, the mite feeding strategy and the host regulation role by the salivary secretions have been poorly explored. Here we contribute to fill this gap by identifying the salivary components of <em>V. destructor </em>and by studying their on mite feeding and survival. Our differential expression analysis identified 30 salivary gland genes encoding putatively secreted proteins, among which only 15 were found to be functionally annotated. These latter include proteins with putative antibacterial, antifungal, cytolytic, digestive and immunosuppressive function. To study the role of the identified genes on mite feeding we selected the three most highly transcribed genes coding for: a chitin-binding domain protein (CHIBIN), a Kazal domain serine protease inhibitor (KAZAL) and a papain-like cysteine protease (PAPA). Knockdown of CHIBIN was associated with a significant decrease of mite survival, likely interfering with the immune reaction to facilitate mite feeding. This work expands our knowledge of the host regulation and nutritional exploitation strategies adopted by ectoparasites of arthropods and allows the identification of novel targets for RNAi-based strategies <span> </span>of <em>Varroa </em>mite control. <span> </span></span></p>
Transcriptome_with_contaminations
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Single-cell transcriptomics data set for plasmodium falciparum 3D7 asexual and sexual stages
Open the record for dataset details and reuse information.
Inorganic biomaterials shape the transcriptome profile to induce endochondral differentiation
<div> <p>Minerals play a vital role, working synergistically with enzymes and other cofactors to regulate physiological functions including tissue healing and regeneration. The bioactive characteristics of mineral-based nanomaterials can be harnessed to facilitate in situ tissue regeneration by attracting endogenous progenitor and stem cells and subsequently directing tissue-specific differentiation. Here, we investigate cellular responses of human mesenchymal stem/stromal cells (hMSCs) to traditional bioactive mineral-based nanomaterials, such as hydroxyapatite (nHA), whitlockite (nWH), silicon-dioxide (nSiO<sub>2</sub>), and the emerging synthetic 2D nanosilicates (nSi). We utilized transcriptome sequencing (RNA-seq) to probe the cellular response and determine the significantly affected signaling pathways due to exposure to these inorganic nanomaterials. Transcriptome profiles of stem cells treated with nanosilicates revealed a stabilized skeletal progenitor state suggestive of endochondral differentiation. This observation is bolstered by enhanced deposition of matrix mineralization in nanosilicate treated stem cells compared to control or other treatments. Specifically, use of 2D nanosilicates directs osteogenic differentiation of stem cells via activation of bone morphogenetic proteins (BMP) and hypoxia-inducible factor 1-alpha (HIF-1<span><span>a</span></span>) signaling pathway. This study provides a holistic transcriptomic insight into nanomaterial-cell interactions and predicts downstream effects of nanomaterial induction of endochondral differentiation.</p> </div>
Spatial domains identification in spatial transcriptomics by domain knowledge-aware and subspace-enhanced graph contrastive learning
<p>We propose a graph contrastive learning framework, GRAS4T, which combines contrastive learning and subspace module to accurately distinguish different spatial domains by capturing tissue microenvironment through self-expressiveness of spots within the same domain. To uncover the pertinent features for spatial domain identification, GRAS4T employs a graph augmentation based on histological images prior, preserving information crucial for the clustering task. Experimental results on 8 ST datasets from 5 different platforms show that GRAS4T outperforms five state-of-the-art competing methods in spatial domain identification. Significantly, GRAS4T excels at separating distinct tissue structures and unveiling more detailed spatial domains. GRAS4T combines the advantages of subspace analysis and graph representation learning with extensibility, making it an ideal framework for ST domain identification.</p>
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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.