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1,554 results for “nucleus”
single-nucleus RNAseq data from female Aedes aegypti antenna
<p>Single-nucleus RNA sequencing data accompanying Herre*, Goldman* et al. (2022), "Non-Canonical Odor Coding in the Mosquito" (https://doi.org/10.1016/j.cell.2022.07.024)</p> <p>For further analysis see: https://github.com/VosshallLab/Younger_Herre_Vosshall2020/tree/main/snRNAseq_SupplementaryData</p> <p>For raw sequencing files see NCBI BioProject: PRJNA794050</p>
Nucleus Absorbed Dose Kernels for Autoradiography
<p>Dose kernels describing S-values to each cell nucleus in a 2D layer of cells from activity of Lu-177 or Ac-225 in the source region of the center cell in units of Gy/Bq/s. The source region is either the cell cytoplasm or the extracellular membrane. Cells are either spherical with a 6.749 um radius, or cubic with a 10.875 um length. The kernels made of spherical cells have pixel sizes of 13.5 x 13.5 um (one cell size), while the kernels made of cubic cells have pixel sizes of 10.9 x 10.9 um (also one cell size). Each cell contains a nucleus, nuclear membrane, cytoplasm, and extracellular membrane.</p>
Medium spiny neuron electrophysiological properties across male rats and female rats in different estrous cycle phases in the nucleus accumbens core: Excitatory synaptic input, action potential, and intrinsic properties
<p>This dataset presents electrophysiological properties from whole-cell patch clamped nucleus accumbens core medium spiny neurons from male rats and female rats recorded in different estrous cycle phases. Excitatory synaptic input, action potential, and intrinsic properties are presented in an analyzed format, as well as the original electrophysiological recordings of each neuron. These data were originally presented across two different papers (Proaño et al., 2018, 2020) and further analyzed in an additional paper (Long et al., 2024), all of which are cited below. These data were key for establishing that nucleus accumbens neuron electrical function changed across the estrous cycle in response to its associated hormones, programming a phase-dependent sex difference in adulthood. This finding provided a new framework for understanding how biological sex and hormone cyclicity regulate the neurons implicated in motivated behaviors and related functions and disorders.</p>
Dataset: Dopamine neurons projecting to medial shell of the nucleus accumbens drive heroin reinforcement.
<p>This dataset contains the data presented in the paper Dopamine neurons projecting to medial shell of the nucleus accumbens drive heroin reinforcement. (doi: 10.7554/eLife.39945 )</p>
The Unreasonable Ineffectiveness of Nucleus Sampling on Mitigating Text Memorization
<p>We present <strong>OpenMemText</strong> a diagnostic dataset with a known distribution of duplicates that gives us some control over the likelihood of memorization of certain parts of the training data. Given this diagnostic dataset, we analyse the text memorization behavior of large language models (LLMs) when subjected to nucleus sampling.</p> <p>Stochastic decoding methods like nucleus sampling are typically applied to overcome issues such as monotonous and repetitive text generation, which are often observed with maximization-based decoding techniques. We hypothesize that nucleus sampling might also reduce the occurrence of memorization patterns, because it could lead to the selection of tokens outside the memorized sequence.</p> <p>See https://github.com/lukaborec/memorization-nucleus-sampling for more information.</p>
Distinct neural population code and causal roles of primate caudate nucleus in multimodal decision-making
<p>To replicate the results in the paper, you should:</p> <ol> <li>Download and then gunzip the dataset.</li> <li>Download the analysis code at https://github.com/ZacZeng/CN-causally-contributes-to-MSDM.</li> <li>Run code as the README in Git says to get figures in the preprint paper (<a href="https://www.biorxiv.org/content/10.1101/2024.09.03.610907v1">Distinct neural manifolds and critical roles of primate caudate nucleus in multimodal decision-making | bioRxiv</a>).</li> </ol>
Spatial Dissection of the Distinct Cellular Responses to Normal Aging and Alzheimer's Disease in Human Prefrontal Cortex at Single-Nucleus Resolution
Open the record for dataset details and reuse information.
Data from: Mapping movement, mood, motivation, and mentation in the subthalamic nucleus
The anatomical connections of the subthalamic nucleus (STN) have driven hypotheses about its functional anatomy, including the hypothesis that the precise anatomical location of STN deep brain stimulation (DBS) contributes to the variability of motor and non-motor responses across Parkinson disease (PD) patients. We previously tested that hypothesis using a three-dimensional (3D) statistical method to interpret the acute effects of unilateral DBS at each patient's clinically optimized DBS settings and active contact. Here we report a similar analysis from a new study in which DBS parameters were standardized and DBS locations were chosen blind to clinical response. In 74 individuals with PD and STN DBS, STN contacts were selected near the dorsal and ventral border of the STN contralateral to the more affected side of the body. Participants were tested off PD medications in each of 3 unilateral DBS conditions (ventral STN DBS, dorsal STN DBS and DBS off) for acute effects on mood, apathy, working memory, response inhibition and motor function. Voltage, frequency, and pulse width were standardized, and participants and raters were blind to condition. In a categorical analysis, both dorsal and ventral STN DBS improved mean motor function without affecting cognitive measures. Ventral STN DBS induced greater improvement in rigidity and anxiety than dorsal STN DBS. In the 3D analysis, contact location was significant for body hypokinesia, rigidity, and resting tremor, with the greatest improvement occurring with DBS in dorsal STN and zona incerta. The 3D results provide new, direct functional evidence for the anatomically-derived model of STN, in which motor function is best represented in dorsal STN. However, our data suggest that functional segregation between motor and non-motor areas of the STN is limited, since locations that induced improvements in motor function and mood overlapped substantially.
FIGURE 5 in Nucleus patterns of zoea I larvae (Crustacea: Decapoda) in the context of taxonomy
FIGURE 5. Telson of Xantho hydrophilus viewed from dorsally (a., c., e.) and Xantho pilipes viewed from ventrally (b., d., f.), corresponding views made with different techniques. a., b. DAPI stained, c., d. conventional light microscopy, e., f. Scanning EM. An, anus; B, bristles; F, furca branch; PLP, posteriolateral process; Ps3-5, pleon segments 3-5; Se, setae; arrowheads, small lateral processes on setae.
FIGURE 4 in Nucleus patterns of zoea I larvae (Crustacea: Decapoda) in the context of taxonomy
FIGURE 4. Telson of Pisidia longicornis viewed from dorsally (a., c., e.) and Porcellana platycheles viewed from ventrally (b., d., f.), corresponding views made with different techniques. (a.,b.) DAPI stained, (c., d.) conventional light microscopy, (e.,f.) Scanning EM. An, anus, PLP, posteriolateral process; Ps4 and Ps5, pleon segments 4 and 5; Se, setae; T, telson.
FIGURE 1 in Nucleus patterns of zoea I larvae (Crustacea: Decapoda) in the context of taxonomy
FIGURE 1. Survey of DAPI stained zoeas. a. Palaemon elegans, viewed from dorsally. b. Porcellana platycheles, viewed from laterally. c. Xantho incisus, viewed from laterally. Arrowheads regions with intensely stained nuclei.
FIGURE 2 in Nucleus patterns of zoea I larvae (Crustacea: Decapoda) in the context of taxonomy
FIGURE 2. Confocal microscopy of telson of Palaemon elegans viewed from dorsally. a., survey of telson, b., detail. Arrowehads, dense arrangement of nuclei at the telson edge (a.) and nucleus clusters at the base of setae (b.); B, bristles; Se, setae.
FIGURE 3 in Nucleus patterns of zoea I larvae (Crustacea: Decapoda) in the context of taxonomy
FIGURE 3. Telson of Palaemon elegans viewed from dorsally (a., c., e.) and Palaemon adspersus viewed from ventrally (b., d., f.), corresponding views made with different techniques. a., b. DAPI stained, c., d. conventional light microscopy, e., f. Scanning EM. An, anus; B, bristles; PLP, posteriolateral process; Ps5 and Ps6, pleon segments 5 and 6; Se, setae; arrowheads, nuclei in setae (b.) and feather-like lateral branches on setae (e.), arrows, dense arrangement of nuclei at the telson edge.
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>
Mouse Kidney Atlas (MKA) & MKA-Extended: Single-cell and single-nucleus reference atlases of the mouse kidney
<p>This deposit contains two linked datasets of the mouse kidney:<br><br></p> <h4><strong>1. MKA (Mouse Kidney Atlas)</strong></h4> <p>A comprehensive reference atlas of the healthy adult mouse kidney, generated by integrating approximately <strong>140,000 cells and nuclei</strong> from <strong>59 publicly available single-cell and single-nucleus RNA-sequencing datasets</strong> across <strong>eight independent studies</strong>.<br>The MKA harmonizes annotations through a <strong>hierarchical cell-type model</strong>, enabling robust cross-study comparisons and accurate labeling of novel or rare cell populations.</p> <ul> <li> <p><strong>Original publication:</strong> Novella-Rausell <em>et al.</em>, <em>iScience</em> (2023). <em>“A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery.” </em>DOI: <a target="_new" rel="noopener">10.1016/j.isci.2023.106877</a></p> </li> <li> <p><strong>Format:</strong> <code>AnnData</code> object (~141,401 observations × 3,000 genes)</p> </li> </ul> <h4><strong>2. MKA-Extended</strong></h4> <p>An expanded version of the MKA. This extended atlas incorporates <strong>immune, injury-induced, and polycystic kidney disease–specific</strong> cellular populations, providing a unified reference for <strong>Tangram-based deconvolution</strong> of spatial transcriptomics datasets.</p> <ul> <li><strong>Original publication: </strong>Yasinoglu <em>et al.</em>, <em>JASN</em>, (2025). <em>“Spatial Transcriptomics Reveals Injured Cells, Signature Genes, and Communication Patterns in the Cyst Microenvironment of Polycystic Kidney Disease.” </em>DOI: 10.1681/ASN.0000000894</li> <li> <p><strong>Format:</strong> <code>AnnData</code> object (~303,791 observations × 12,156 genes)</p> </li> </ul>
Arginine-vasopressin expressing neurons in the murine suprachiasmatic nucleus exhibit a circadian rhythm in network coherence in vivo
<p>The suprachiasmatic nucleus (SCN) is composed of functionally distinct subpopulations of GABAergic neurons which form a neural network responsible for synchronizing most physiological and behavioral circadian rhythms in mammals. To date, little is known regarding which aspects of SCN rhythmicity are generated by individual SCN neurons, and which aspects result from neuronal interaction within a network. Here, we utilize in vivo miniaturized microscopy to measure fluorescent GCaMP-reported calcium dynamics in arginine vasopressin (AVP)-expressing neurons in the intact SCN of awake, behaving mice. We report that SCN AVP neurons exhibit periodic, slow calcium waves which we demonstrate, using in vivo electrical recordings, likely reflect burst firing. Further, we observe substantial heterogeneity of function in that AVP neurons exhibit unstable rhythms and relatively weak rhythmicity at the population level. Network analysis reveals that correlated cellular behavior, or coherence, among neuron pairs also exhibited stochastic rhythms with about 33% of pairs rhythmic at any time. Unlike single-cell variables, coherence exhibited a strong rhythm at the population level with time of maximal coherence among AVP neuronal pairs at CT/ZT 6 and 9, coinciding with the timing of maximal neuronal activity for the SCN as a whole. These results demonstrate robust circadian variation in the coordination between stochastically rhythmic neurons and interactions between AVP neurons in the SCN may be more influential than single-cell activity in the regulation of circadian rhythms. Furthermore, they demonstrate that cells in this circuit, like those in many other circuits<span></span>, exhibit profound heterogenicity of function over time and space.</p>
Data for: Microglia phagocytosis determines the volume and function of the rat Sexually Dimorphic Nucleus of the Preoptic Area
<p>The Sexually Dimorphic Nucleus of the Preoptic Area (SDN-POA) is the oldest and most robust sex difference reported in mammalian brain and is singular for its presence across a wide range of species from rodents to ungulates to man. This small collection of Nissl dense neurons is reliably larger in volume in males. Yet, despite its notoriety and intense interrogation, both the mechanism establishing the sex difference and the functional role of the SDN have remained elusive. Convergent evidence from rodent studies led to the conclusion that testicular androgens aromatized to estrogens are neuroprotective in males and that higher apoptosis (naturally occurring cell death) in females determines their smaller SDN. In several species, including humans, a smaller SDN correlates with a preference for mating with males. We report here that this volume difference is dependent upon a participatory role of phagocytic microglia which engulf more neurons in the female SDN and assure their destruction . Selectively blocking microglia phagocytosis temporarily spared neurons from apoptotic death and increased SDN volume in females without hormone treatment. Increasing the number of neurons in the SDN in neonatal females resulted in loss of preference for male odors in adulthood, an effect paralleled by dampened excitation of SDN neurons as evidenced by reduced IEG expression when exposed to male urine. Thus, the mechanism establishing a sex difference in SDN volume includes an essential role for microglia, and SDN function as a regulator of sexual partner preference is confirmed.</p>
Single-nucleus RNA-sequencing reveals oligodendrocytes and their progenitors as vulnerable cell types in prefrontal cortex and anterior cingulate of brains with Parkinson's disease
<p>Several prior studies have proposed the involvement of various brain regions and cell types in Parkinson's disease (PD) pathology. Here, we performed snRNA-seq on the prefrontal cortex and anterior cingulate regions from post-mortem control and PD brain tissue. We found a dramatic association of oligodendrocytes and oligodendrocyte precursor cells with PD-linked risk loci and reported several dysregulated genes and pathways, including regulation of tau-protein kinase activity, regulation of inclusion body assembly and protein processing involved in protein targeting to mitochondria.</p>
Dopamine in the Dorsal Bed Nucleus of Stria Terminalis signals Pavlovian sign-tracking and reward violations
<p>Raw data associated with Gyawali et al., 2022</p>
Impact of Deep Brain Stimulation of Subthalamic Nucleus on the Hepatic Glucose Production in Parkinson's Disease
ClinicalTrials.gov study NCT00663312. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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.