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2,326 results for “clusters”
Cell type labels for all clustering and normalization combinations compared for CODEX multiplexed imaging
<p>We performed CODEX (co-detection by indexing) multiplexed imaging on four sections of the human colon (ascending, transverse, descending, and sigmoid) using a panel of 47 oligonucleotide-barcoded antibodies. Subsequently images underwent standard CODEX image processing (tile stitching, drift compensation, cycle concatenation, background subtraction, deconvolution, and determination of best focal plane), and single cell segmentation. Output of this process was a dataframe of nearly 130,000 cells with fluorescence values quantified from each marker. We used this dataframe as input to 1 of the 5 normalization techniques of which we compared z, double-log(z), min/max, and arcsinh normalizations to the original unmodified dataset. We used these normalized dataframes as inputs for 4 unsupervised clustering algorithms: k-means, leiden, X-shift euclidian, and X-shift angular.</p> <p>From the clustering outputs, we then labeled the clusters that resulted for cells observed in the data producing 20 unique cell type labels. We also labeled cell types by hiearchical hand-gating data within cellengine (cellengine.com). We also created another gold standard for comparison by overclustering unormalized data with X-shift angular clustering. Finally, we created one last label as the major cell type call from each cell from all 21 cell type labels in the dataset. </p> <p>Consequently the dataset has individual cells segmented out in each row. Then there are columns for the X, Y position in pixels in the overall montage image of the dataset. There are also columns to indicate which region the data came from (4 total). The rest are labels generated by all the clustering and normalization techniques used in the manuscript and what were compared to each other. These also were the data that were used for neighborhood analysis for the last figure of the manuscript. These are provided at all four levels of cell type level granularity (from 7 cell types to 35 cell types). </p>
Lattice kinetic Monte Carlo model to simulate RNA polymerase II clusters
<p>This data set includes Python scripts (numerical simulation and analysis) and already generated simulation data for RNA polymerase II clusters. RNA polymerase II particles as single lattice sites and chromatin with regulatory region as connected polymer.</p>
Clustering of Catalytic Nanocompartments for Enhancing an Extracellular Non-Native Cascade Reaction
<p>Data underlying the figures in the publication “Clustering of Catalytic Nanocompartments for Enhancing an Extracellular Non-Native Cascade Reaction”, published in <em>Chemical Science</em> <strong>2021</strong>.</p> <p>Table of contents:</p> <p><strong>1. Figure 2</strong>; Zip. archive containing the experimental data of the graphs in <em>Figure 2</em>.</p> <p><strong>2. Figure 3</strong>; Zip. archive containing the experimental data of the graphs in <em>Figure 3</em>.</p> <p><strong>3. Figure 4</strong>; Zip. archive containing the experimental data of the graphs in <em>Figure 4</em>.</p> <p><strong>4. Figure 5</strong>; Zip. archive containing the experimental data of the graphs in <em>Figure 5</em>.</p> <p><strong>5. Figure 7</strong>; Zip. archive containing the experimental data of the graphs in <em>Figure 7</em>.</p>
Microscopy data: interaction of the gene ripply1 with RNA polymerase II clusters during early zebrafish embryo development
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>ripply1</em> and is obtained from fixed zebrafish embryos, collected at the developmental stages oblong, sphere, dome, 30% epiboly, and 50% epiboly (indicated in the file names). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two independent experiments were performed (IF1, IF2 in the file name), for each experiment, two samples were prepared per stage and experiment (001, 002 in the file name).</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data: interaction of the gene klf2b with RNA polymerase II clusters during early zebrafish embryo development
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>klf2b</em> and is obtained from fixed zebrafish embryos, collected at the developmental stages oblong, sphere, dome, 30% epiboly, and 50% epiboly (indicated in the file names). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two independent experiments were performed (IF1, IF2 in the file name), for each experiment, one or two samples were prepared per stage and experiment (001, 002 in the file name).</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data: interaction of the gene foxd5 with RNA polymerase II clusters during early zebrafish embryo development
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>foxd5</em> and is obtained from fixed zebrafish embryos, collected at the developmental stages oblong, sphere, dome, 30% epiboly, and 50% epiboly (indicated in the file names). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two independent experiments were performed (IF1, IF2 in the file name), for each experiment, two or three samples were prepared per stage and experiment (001, 002 in the file name).</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data: interaction of the gene gadd45ga with RNA polymerase II clusters during early zebrafish embryo development
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>gadd45ga</em> and is obtained from fixed zebrafish embryos, collected at the developmental stages oblong, sphere, dome, 30% epiboly, and 50% epiboly (indicated in the file names). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two independent experiments were performed (IF1, IF2 in the file name), for each experiment, two samples were prepared per stage and experiment (001, 002 in the file name).</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data: interaction of the gene drll2 with RNA polymerase II clusters during early zebrafish embryo development
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>drll2</em> and is obtained from fixed zebrafish embryos, collected at the developmental stages oblong, sphere, dome, 30% epiboly, and 50% epiboly (indicated in the file names). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two independent experiments were performed (IF1, IF2 in the file name), for each experiment, two samples were prepared per stage and experiment (001, 002 in the file name).</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data: interaction of the gene iscub with RNA polymerase II clusters during early zebrafish embryo development
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>iscub</em> and is obtained from fixed zebrafish embryos, collected at the developmental stages oblong, sphere, dome, 30% epiboly, and 50% epiboly (indicated in the file names). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two independent experiments were performed (IF1, IF2 in the file name), for each experiment, two samples were prepared per stage and experiment (001, 002 in the file name).</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
IsoAnalyst: A System-Wide Stable Isotopic Labeling Aproach for Connecting Natural Products to Their Cognate Biosynthetic Gene Clusters
<p>Processed mass spectrometry data input used to develop and validate the IsoAnalyst program and the output from these analyses. The S_erythraea folder contains all MS input and output data for <em>Saccharopolyspora erythraea</em>. The Micromonospora_RL09050HVFA folder contains MS input and output data for <em>Micromonopora sp.</em> RL09050HVFA, as well as the full antiSMASH output for the <em>Micromonopora sp.</em> RL09050HVFA genome.</p> <p>Version 2 contains updated IsoAnalyst results for both organisms. </p>
Dataset for "A novel method to identify sub-seasonal clustering episodes of extreme precipitation events and their contributions to large accumulation periods"
<p>Dataset for "A novel method to identify sub-seasonal clustering episodes of extreme precipitation events and their contributions to large accumulation periods".</p> <p>Added file "Obs_metrics_all.RData" containing p-value for significance test of the clustering metric S_cl.</p> <p>Accepted version (August 2021).</p>
Hubble Frontier Field Clusters and their Parallel Fields: Photometric and Photometric Redshift Catalogs
<p>Source catalogs of the Hubble Frontier Field clusters and parallel fields. If used, please cite https://ui.adsabs.harvard.edu/abs/2021arXiv210301952P/abstract</p>
Supporting data for the manuscript "Nerpa: a tool for discovering biosynthetic gene clusters of nonribosomal peptides"
<p>Preprocessed structures of nonribosomal peptides [NRPs] and genomic sequences (reference and representative genomes, biosynthetic gene clusters [BGCs]) used in the benchmark experiments in the Nerpa paper.</p> <p><strong>Files description</strong></p> <ul> <li><strong>mibig_nrp_bacteria_preprocessed.tar.gz</strong> contains the preprocessed dataset of 194 bacterial NRP BGCs from the MIBiG database.</li> <li><strong>mibig_nrp_bacteria_summary.tsv</strong> contains metadata for the MIBiG-NRP dataset.</li> <li><strong>bacterial_ref_and_repr_genomes_20210604_preprocessed.tar.gz</strong> contains the preprocessed dataset of 13,399 reference and representative bacterial genomes from the NCBI RefSeq database (retrieved on 2021/06/04).</li> <li><strong>bacterial_ref_and_repr_genomes_20210604_summary.txt</strong> contains metadata for the RefSeq dataset.</li> <li><strong>pnrpdb_preprocessed.info</strong> contains the Nerpa-preprocessed pNRPdb database, a database of 8,368 known and putative NRP structures.</li> <li><strong>pnrpdb_summary.tsv</strong> contains the pNRPdb database metadata.<br> </li> </ul>
3D microelectrode cluster and stimulation paradigm yield powerful analgesia without noticeable adverse effects
<p>The dataset contains the underlying data for the figures in the paper "3D microelectrode cluster and stimulation paradigm yield powerful analgesia without noticeable adverse effects" by M. Forni et al., Science Advances, 2021. In the reported study, we present a newly developed biocompatible gelatin-embedded cluster of microelectrodes that enable higly customizable stimulation in the periaqueductal gray/dorsal raphe nucleus in awake rats. We were able to select a subset of electrodes for each individual, that upon stimulation provided significant pain inhibition during both normal and hyperalgesia conditions, without noticable side effects.</p> <p>Pain responses were quantified in terms of evoked field potentials (FP) and neuronal activity (z score), as well as withdrawal rate (WR) resulting from stimulating the skin with either a CO2-laser or a tactile stimulator, and analyzed with respect to multiple variables, such as time from stimulation onset, effect in comparison to morphine administration etc. Also, the effects of stimulation were quantified in terms of gait parameters (speed and paw-usage symmetry).</p> <p>The location of implanted electrodes was verified using computed tomography (CT) imaging and superimposition to the Waxholm brain atlas. The dataset contains the CT images for each anaimal, as obtained after alignment to the atlas.</p>
Clustering of loci controlling species differences in male chemical bouquets of sympatric Heliconius butterflies
<p>The degree to which loci promoting reproductive isolation cluster in the genome – <i>i.e. </i>the genetic architecture of reproductive isolation - can influence the tempo and mode of speciation. Tight linkage between these loci can facilitate speciation in the face of gene flow. Pheromones play a role in reproductive isolation in many Lepidoptera species, and the role of endogenously-produced compounds as secondary metabolites decreases the likelihood of pleiotropy associated with many barrier loci. <i>Heliconius </i>butterflies use male sex pheromones to both court females (aphrodisiac wing pheromones) and ward off male courtship (male-transferred anti-aphrodisiac genital pheromones), and it is likely that these compounds play a role in reproductive isolation between <i>Heliconius </i>species. Using a set of backcross hybrids between <i>H. melpomene </i>and <i>H. cydno</i>, we investigated the genetic architecture of putative male pheromone compound production. We found a set of 40 significant quantitative trait loci (QTL) representing 33 potential pheromone compounds. QTL clustered significantly on two chromosomes, chromosome 8 for genital compounds and chromosome 20 for wing compounds, and chromosome 20 was enriched for potential pheromone biosynthesis genes. There was minimal overlap between pheromone QTL and known QTL for mate choice and color pattern. Nonetheless, we did detect linkage between a QTL for wing androconial area and <i>optix</i>, a color pattern locus known to play a role in reproductive isolation in these species. This tight clustering of putative pheromone loci might contribute to coincident reproductive isolating barriers, facilitating speciation despite ongoing gene flow.</p>
Towards highly accurate calculations of parity violation in chiral molecules: relativistic coupled-cluster method including QED-effects
<p>This dataset collects the unprocessed (= outputs from calculations) results discussed in the paper titled "Towards highly accurate calculations of parity violation in chiral molecules: relativistic coupled-cluster method including QED-effects", by Ayaki Sunaga and Trond Saue.</p>
Galaxy clustering in real space
<p>Galaxy clustering in real space from BAM galaxy catalogs. Marked and two point correlation function0</p>
Seismic Magnitude Clustering is Prevalent in Field and Laboratory Catalogs [DATA]
<p>Catalogs for Nature Communications article: Seismic Magnitude Clustering is Prevalent in Field and Laboratory Catalogs.</p> <p> </p> <p>Update: In DataVariableExplanation, two catalogs from University of Minnesota</p> <p>Mixed mode and mode I bending data description needs to show that the third column is in seconds.</p>
Internal proper motion dispersion profiles for 37 Milky Way globular clusters extracted from Gaia EDR3
<p>Internal proper motion dispersion profiles, in the radial and tangential components, extracted from Gaia EDR3 data for 37 Milky Way globular clusters.</p> <p>Created for, and used for model fitting in, the submitted manuscript: "Multimass modelling of Milky Way globular clusters - I. Implications on their stellar initial mass function above 1 M$_{\odot}$". Details on the creation of this dataset are available within this article.</p>
A Photometric Survey of Globular Cluster Systems in Brightest Cluster Galaxies
<p>Complete photometry and reference images from HST, for globular cluster systems around 26 giant early-type galaxies.</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.