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Data from: Clathrin-independent endocytic retrieval of SV proteins mediated by the clathrin adaptor AP-2 at mammalian central synapses
<p><span>Neurotransmission is based on the exocytic fusion of synaptic vesicles (SVs) followed by endocytic membrane retrieval and the reformation of SVs. Conflicting models have been proposed regarding the mechanisms of SV endocytosis, most notably clathrin/ AP-2-mediated endocytosis and clathrin-independent ultrafast endocytosis. Partitioning between these pathways has been suggested to be controlled by temperature and stimulus paradigm. We report on the comprehensive survey of six major SV proteins to show that SV endocytosis in mouse hippocampal neurons at physiological temperature occurs independent of clathrin while the endocytic retrieval of a subset of SV proteins including the vesicular transporters for glutamate and GABA depend on sorting by the clathrin adaptor AP-2. Our findings highlight a clathrin-independent role of the clathrin adaptor AP-2 in the endocytic retrieval of select SV cargos from the presynaptic cell surface and suggest a revised model for the endocytosis of SV membranes at mammalian central synapses.</span></p>
Data from: Population genetics and independently replicated evolution of predator-associated burst speed ecophenotypy in mosquitofish
<p>Many species show replicated ecophenotypy due to recurring patterns of natural selection. Based on the presence or absence of pursuit predators, at least 17 species of fish repeatedly differentiated in body shape in a manner that increases burst swimming speed and the likelihood of predator escape. The predator-associated burst speed (<b>PABS</b>) ecophenotype is characterized by a small head and trunk and enlarged caudal region. Mechanisms promoting replicated phenotype-environment association include selection (without evolution), a single instance of adaptive evolution followed by biased habitat occupation, repeated instances of local adaptation, or adaptive phenotypic plasticity. Common garden rearing of mosquitofish, <i>Gambusia affinis</i>, demonstrated a likely heritable basis for PABS phenotypy, but it is unknown whether populations are otherwise genetically distinct or whether replicated ecophenotypy represents a single or replicated instances of adaptation. To genetically characterize the populations and test hypotheses of single or multiple adaptations, we characterized variation in 12 polymorphic DNA microsatellites in the previously studied <i>G. affinis</i> populations. Populations were genetically distinct by multilocus analysis, exhibited high allelic diversity, and were heterozygote deficient, which effects were attributed to <i>G. affinis</i>'s shoaling nature and habitat patchiness. Genetic and phenotypic distances among populations were correlated for non-PABS but not PABS morphology. Multilocus analysis demonstrated ecophenotype polyphyly and scattered multivariate genetic structure which support only the replicated-adaptation model. As all of the diverse tests performed demonstrated lack of congruence between patterns of molecular genetic and PABS differentiation, it is likely that divergent natural selection drove multiple instances of adaptive evolution.Many species show replicated ecophenotypy due to recurring patterns of natural selection. Based on the presence or absence of pursuit predators, at least 17 species of fish repeatedly differentiated in body shape in a manner that increases burst swimming speed and the likelihood of predator escape. The predator-associated burst speed (<b>PABS</b>) ecophenotype is characterized by a small head and trunk and enlarged caudal region. Mechanisms promoting replicated phenotype-environment association include selection (without evolution), a single instance of adaptive evolution followed by biased habitat occupation, repeated instances of local adaptation, or adaptive phenotypic plasticity. Common garden rearing of mosquitofish, <i>Gambusia affinis</i>, demonstrated a likely heritable basis for PABS phenotypy, but it is unknown whether populations are otherwise genetically distinct or whether replicated ecophenotypy represents a single or replicated instances of adaptation. To genetically characterize the populations and test hypotheses of single or multiple adaptations, we characterized variation in 12 polymorphic DNA microsatellites in the previously studied <i>G. affinis</i> populations. Populations were genetically distinct by multilocus analysis, exhibited high allelic diversity, and were heterozygote deficient, which effects were attributed to <i>G. affinis</i>'s shoaling nature and habitat patchiness. Genetic and phenotypic distances among populations were correlated for non-PABS but not PABS morphology. Multilocus analysis demonstrated ecophenotype polyphyly and scattered multivariate genetic structure which support only the replicated-adaptation model. As all of the diverse tests performed demonstrated lack of congruence between patterns of molecular genetic and PABS differentiation, it is likely that divergent natural selection drove multiple instances of adaptive evolution.</p>
Supplementary Data for: Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches
<p><strong>Supplementary Data</strong></p> <p><strong>Tables</strong></p> <p><strong>Table S1:</strong> Virus characteristics including abbreviation, family, order, tax id, sequence length threshold (for nearly complete genomes), vaccination status, mode of transmission, circulation (human or human/zoonotic), available treatment, and disease progression (acute or chronic).</p> <p><strong>Table S2:</strong> Sequence IDs of outgroup constituents.</p> <p><strong>Table S3:</strong> GISAID acknowledgements for the SARS-CoV-2 sequences used in this study.</p> <p><strong>Table S4:</strong> Summary of manual sequence curation indicating lab- or vaccine-related keywords used to prune sequences.</p> <p><strong>Table S5:</strong> Sequence IDs for EVA and H3N2 e10, e100, d10, and d100 subtrees.</p> <p><strong>Table S6:</strong> Sequence IDs for ML and GL lineages.</p> <p><strong>Table S7:</strong> Sequence IDs for the H3N2 “new” and “old” subtrees.</p> <p><strong>Table S8:</strong> Mutation rates (in units of nucleotide substitutions per site per year) and estimated dates for the last common ancestor of all tree/subtrees. Negative dates represent years prior to 0 CE.</p> <p><strong>Table S9:</strong> Mean dN/dS values.</p> <p><strong>Table S10:</strong> Yearly viral cases and generation time estimations (with references).</p> <p><strong>Table S11:</strong> Metadata including the sequence ID, host, date of isolation, location of isolation, and subtype.</p> <p><strong>Table S12:</strong> Overview of key parameters including number of GLs N, Ne, and MRCA for each virus species as well as the mean over all species.</p> <p><strong>Directories</strong></p> <p><strong>Alignments</strong> ORFeome alignments (excluding stop codons) with the exception of SARS-CoV-2.</p> <p><strong>Correlated Subtrees</strong> Subtrees representing all correlated-clades (genealogical lineages; GL) in Newick format.</p> <p><strong>Diversity TMRCA and Skyline Plots</strong> .png files.</p> <p><strong>e/d/n/o Subtrees</strong> EVA and H3N2 subtrees, evenly and diversely sampled as well as “early” and “late” subtrees for H3N2.</p> <p><strong>Genealogical Trees</strong> Including global topologies (.main), subtrees, and grafted trees (.grafted).</p> <p><strong>Maximally Diverse Subtrees:</strong> Genealogical trees sampled to contain the same number of leaves as each respective tree in the Simulated Trees directory.</p> <p><strong>ORF References</strong> The first and last nucleotide of each ORF in the reference sequence.</p> <p><strong>Redundancy Tables</strong> List of all redundant isolates and the corresponding representative in the ORFeome-unique alignment.</p> <p><strong>Reference Sequences</strong> Genbank page for all reference sequences.</p> <p><strong>Rooted Trees</strong> Global topologies for each virus.</p> <p><strong>Simulated Trees:</strong> Neutral models, based on Yule-Harding, for each virus.<br> Ultrametric Trees For each global topology.</p> <p><strong>Ultrametric Trees </strong>For each global topology.</p>
Observational Dataset for "Constraining Global Coronal Models with Multiple Independent Observables", Badman et al. (2022). Arxiv : https://arxiv.org/abs/2201.11818
<p>Observational Dataset for "Constraining Global Coronal Models with Multiple Independent Observables", Badman et al. (2022). Arxiv : https://arxiv.org/abs/2201.11818</p> <p>-----------------------------<br> -----------------------------</p> <p>Contact : Samuel T. Badman (he/him) samuel_badman@berkeley.edu, Space Sciences Lab, UC Berkeley.</p> <p>-----------------------------<br> -----------------------------</p> <p>License : Creative Commons Attribution 4.0 International</p> <p>-----------------------------<br> -----------------------------</p> <p>Research Goal of Dataset : Data supports the above titled work in defining a framework for evaluating the magnetic structure of global coronal models via the evaluation of three single valued metrics. This repository contains observational data products used as input for the studies described in this work with the aim to allow external coronal modelers to reproduce and evaluate their own work against the same dataset we used.</p> <p>-----------------------------<br> -----------------------------</p> <p>Structure of files : This repository contains three subfolders each containing observational data relating to the three metrics defined in Badman et. al. (2022). These are :</p> <p>-----------------------------</p> <p>1) ``Metric1_EUVCarringtonMaps''</p> <p>Content :</p> <p><carr_maps.####.final.h5> : Carrington maps of extreme ultraviolet (EUV) emission as observed by the SDO/AIA. These files contain slices of different wavelengths together, saved in hdf5 format. Maps for Carrington rotations (#### = 2210,2215,2216,2221) span the time intervals of interest in the associated work. The 193 angstrom wavelength slice from these maps were used as input into the EZSEG algorithm (see manuscript text) to generate ``observations'' of coronal hole boundaries which can then be compared via binary classification to modeled open field boundaries.</p> <p><read_plot_example_metric1.py> : A python script which demonstrates reading in the hdf5 files and viewing the names of the different slices, then plots the 193 slice. The slice name of primary interest is 193A ('map_0193'), but slices at 171,211 angstrom, and a magnetogram are included.</p> <p>-----------------------------</p> <p>2) ``Metric2_StreamerBelt''</p> <p><read_plot_example_metric2.py> : A python script which demonstrates reading and plotting an example white light carrington map from this data set, as well as overplotting the downstream data extraction of the streamer maximum brightness (SMB) line.</p> <p><br> 2a) ``Metric2_StreamerBelt/WL_CarringtonMaps''</p> <p>Content :</p> <p><WL_CRMAP_YYYYMMDDTHHmmSS_LC2_5p0Rs.fits> : Carrington maps of white light intensity extracted at 5.0Rs altitude using coronagraph images taken by SOHO/LASCO, using the method described in the manuscript and Poirier et al. (2021). Maps at a daily cadence over each 60 day time interval studied in the manuscript are included here, incorporating the new data available as the sun rotated. Here saved as fits files.</p> <p><WL_CRMAP_YYYYMMDDTHHMMSS_LC2_5p0Rs.mat> : Carrington maps as above but saved in .mat format (MATLAB).</p> <p>2b) ``Metric2_StreamerBelt/SMB_Line_Extractions''</p> <p><C2_YYYMMDDHHmmSS_5.0Rs_SMB.ascii> : Downstream processed versions of the relevant White light carrington map from which the line of maximum brightness (SMB line) has been extracted, as well as the streamer belt "thickness" at each longitude. This is tabulated as a 3d coordinate gridded evenly in longitude, and each SMB grid point as a northwards and southwards thickness, tabulated in degrees. These data are described in the header of each file and the extraction process is described in detail in the manuscript.</p> <p>-----------------------------</p> <p>3)Metric3_InSituTimeSeries</p> <p>Content :</p> <p><E##_XYZ_polarity.txt> : In situ polarity timeseries for 60 day intervals at 1 hour cadences during PSP encounters ## = [01,02,03], measured by spacecraft XYZ = [PSP,STA,OMN], Parker Solar Probe, STEREO A and OMNI (Earth-L1 dataset). Data values are +/- 1 indicating if magnetic vector is directed sunward or antisunward for each hour. This value is determined as described in the main text by finding the peak of a histogram of 1D B_R values over that hour interval and taking its sign.</p> <p><read_plot_example_metric3.py> : A python script which demonstrates reading in the in situ timeseries for encounter 1 and plotting them.</p> <p><gen_ss_footpoints_psp.py> : A python script which demonstrates an open source method to produce source surface footpoints for a given spacecraft (here PSP) which can be used to sub-sample a HCS map provided by a modeler to generate a modeled time series which can be used to produce scores for metric 3 described in the associated manuscript.</p> <p>-----------------------------<br> -----------------------------</p> <p>Python scripts included in this dataset use python packages</p> <p>astropy - https://github.com/astropy/astropy<br> h5py - https://github.com/h5py/h5py<br> astrospice - https://github.com/dstansby/astrospice<br> matplotlib - https://github.com/matplotlib/matplotlib<br> sunpy - https://github.com/sunpy/sunpy</p> <p> </p> <p> </p>
Independence of mate choice components (choosiness and preference functions) in Hyla versicolor
<p>Mate choice is an important cause of natural and sexual selection, driving the evolution of ornaments and promoting diversification and speciation. Mate choice decisions arise from the interaction of several components, and knowledge of whether they interact, and how, is crucial for understanding their contributions to selection. Here we focus on the relationship between preference functions (attractiveness ranking of prospective mates) and choosiness (effort invested in obtaining the preferred mate) and test the hypothesis that they are independent components of mate choice decisions. We examine individual variation in preference functions and choosiness for call duration in female <em>Hyla versicolor </em>treefrogs, and show that measures describing preference functions and choosiness are not correlated. We also found a suggestive but inconclusive pattern that both components are influenced by different factors (body measures and hormones). Independence of preference and choosiness suggests that the joint study of variation in both components is required to gain a complete understanding of how mate choice contributes to sexual selection and speciation.</p>
Data from: Independent evolution of highly variable, fragmented mitogenomes of parasitic lice
<p>The mitochondrial genomes (mitogenomes) of bilaterian animals are highly conserved structures that usually consist of a single circular chromosome. However, several species of parasitic lice (Insecta: Phthiraptera) possess fragmented mitogenomes, where the mitochondrial genes are present on separate, circular chromosomes. Nevertheless, the extent, causes, and consequences of this structural variation remain poorly understood. Here, we combined new and existing data to better understand the evolution of mitogenome fragmentation in major groups of parasitic lice. We found strong evidence that fragmented mitogenomes evolved many times within parasitic lice and that the level of fragmentation is highly variable, including examples of heteroplasmic arrangements. We also found a significant association between mitochondrial fragmentation and signatures of relaxed selection. Mitochondrial fragmentation was also associated with changes to a lower AT%, possibly due to differences in mutation biases. Together, our results provide a significant advance in understanding the process of mitogenome fragmentation and provide an important perspective on mitochondrial evolution in eukaryotes.</p>
Genome and gene annotation for yeast strain SK1 used in "Deciphering the "m6A Code" via Antibody-Independent Quantitative Profiling"
<p>Genome and gene annotation used in "Deciphering the “m6A Code” via Antibody-Independent Quantitative Profiling" provided by Schraga Schwartz from his time at the Broad Institute.</p>
Data from: IFN-γ-independent control of M. tuberculosis requires CD4 T cell-derived GM-CSF and activation of HIF-1α
<p><strong>RNA sequencing dataset from "Van Dis et al., IFN-γ-independent control of M. tuberculosis requires CD4 T cell-derived GM-CSF and activation of HIF-1α. 2022"</strong></p> <p>The prevailing model of protective immunity to tuberculosis is that CD4 T cells produce the cytokine IFN-γ to activate bactericidal mechanisms in infected macrophages. Although IFN-γ-independent CD4 T cell based control of <em>M. tuberculosis</em> infection has been demonstrated <em>in vivo</em> it is unclear whether CD4 T cells are capable of directly activating macrophages to control infection in the absence of IFN-γ. We developed a co-culture model using CD4 T cells isolated from the lungs of infected mice and <em>M. tuberculosis</em>-infected murine bone marrow-derived macrophages (BMDMs) to investigate mechanisms of CD4 dependent control of infection. This dataset represents RNA sequencing data from M. tuberculosis-infected wild-type and <em>Ifngr-/- </em>murine bone marrow-derived macrophages (BMDMs) after 24 hours of lung CD4 T cell co-culture.</p> <p>CD4 T cells induced differential regulation of 1825 genes in wild-type BMDMs and 1142 genes in <em>Ifngr-/-</em> BMDMs compared to untreated. Although wild-type and <em>Ifngr-/-</em> BMDMs infected with <em>M. tuberculosis</em> were transcriptionally very similar prior to activation, the transcriptome of these genotypes of macrophages diverged after CD4 T cell co-culture. This is likely due in part to the presence or absence of IFN-γ signaling as IFN-γ alone regulates the expression of >2500 genes during <em>M. tuberculosis</em> infection. Still, 769 genes were altered in an IFN-γ-independent manner, with >2-fold upregulation in both wild-type and <em>Ifngr-/- </em>BMDMs. We found no difference in macrophage polarization between untreated M. tuberculosis-infected wild-type and <em>Ifngr-/-</em> BMDMs, and no significant increase in the expression of genes associated with M2 macrophages after CD4 T cell co-culture in either genotype. However, there was significant upregulation of genes associated with M1 macrophages after CD4 T cell co-culture in both genotypes, with wild-type BMDMs slightly more polarized. Collectively, these results show comparable patterns of activation in wild-type and <em>Ifngr-/-</em> macrophage during CD4 T cell co-culture, indicating that CD4 T cells elicit significant polarizing, inflammatory and antimicrobial effects in <em>M. tuberculosis</em>-infected macrophages irrespective of IFN-γ signaling.</p>
PD1+CD8+ cells are an independent prognostic marker in patients with head and neck cancer
<p><strong>Data open:</strong> file with parametres used for the multivariate evaluation. </p>
Proclamation of Free and Independent Poland
Medal of the Proclamation of Free and Independent Poland ID no.: MNS-H/123 Museum: Nowy Sącz District Museum http://muzea.malopolska.pl/en/o-nas Digitalisation: RDW MIC, Virtual Małopolska project Source: Objaverse 1.0 / Sketchfab
Independence Monument, Kyiv
Monument of Independence, Kyiv. You are free to use it for whatever you wish. If you want to share with us what you use it for that would be awesome 😁 We modelled it for an AR artistic installation where people could place the monument in their city centers and plazas, realising Ukraine's fight is also for protecting the other democratic countries. (Especially us, being based in Romania). Source: Objaverse 1.0 / Sketchfab
When the Dragons Defeat the Knight: Basilisk an Architectural Pattern for Platform and Language Independent Development
<p>Experimental dataset and the scripts needed to run the experiment described in the paper:</p> <p><strong> When the Dragons Defeat the Knight</strong>: <br> Basilisk an Architectural Pattern for Platform and Language Independent Development<br><em> Francesco Bertolotti, Walter Cazzola, Dario Ostuni</em> and <em>Carlo Castoldi</em></p> <p>Published in Journal of Systems and Software, 215, September 2024. Elsevier.</p>
Enhancing Full Waveform Inversion of Field GPR Data: A Source-Independent Approach with Dynamic Reference Selection via SE-Wave-U-Net
<p>Data presented in the manuscript titled 'Enhancing Full Waveform Inversion of Field GPR Data: A Source-Independent Approach with Dynamic Reference Selection via SE-Wave-U-Net'</p>
Data from: Environmentally independent selection for hybrids between divergent freshwater stickleback lineages in semi-natural ponds
<p>Hybridization following secondary contact of genetically divergent populations can influence the range expansion of invasive species, though specific outcomes depend on the environmental dependence of hybrid fitness. Here, using two genetically and ecologically divergent threespine stickleback lineages that differ in their history of freshwater colonization, we estimate fitness variation of parental lineages and hybrids in semi-natural freshwater ponds with contrasting histories of nutrient loading. In our experiment, we found that fish from the older freshwater lineage (Lake Geneva) and hybrids outperformed fish from the younger freshwater lineage (Lake Constance) in terms of both growth and survival, regardless of the environmental context of our ponds. Across all ponds, hybrids exhibited the highest survival. Although wild- caught adult populations differed in their functional and defence morphology, it is unclear which of these traits underlie the fitness differences observed among juveniles in our experiment. Overall, our work suggests that when hybrid fitness is insensitive to environmental conditions, as observed here, introgression may promote population-expansion into unoccupied habitats and accelerate invasion success.</p>
Statistical learning shapes pain perception and prediction independently of external cues
<h1>Dataset and code for the relevant analysis and results:</h1> <h3>"Statistical learning shapes pain perception and prediction independently of external cues"</h3> <p>Onysk, J., Whitefield, M., Gregory, N., Jain, M., Turner, G., Seymour, B., Mancini, F. (2024). eLife. <a href="https://doi.org/10.7554/eLife.90634.2">https://doi.org/10.7554/eLife.90634.2</a></p> <h2>1 - data_collection</h2> <p>Contains the code for the psychophysical experiment (PsychToolBox), including the sequence generations scripts.</p> <h2>2 - preprocessing</h2> <p>Contains code that preprocesses behavioural data from PsychToolBox. This includes linear transformation of inputs, exporting data to stan readable format and plotting Supplement figures.</p> <p>- The raw behavioural data can be found in <strong><em>preprocessing/data</em></strong>. Stan ready ready for each condition is found in <strong><em>preprocessing/stan_data</em></strong></p> <h2>3 - model_fit_analysis</h2> <p>Contains stan models used in the paper ('models/'), model fitting code ('fit_models_cs.R) (inlcuding HPC setup in 'hpc/'), initial analysis script for processing stan samples ('primary_analysis_cs.R'), as well as additional analyis scripts ('extra_analysis_cs.R', 'correlation_beh_model_cs.ipynb') that generate figures from the paper and supplement.</p> <p>- The posterior draws for parameters can be found in <em><strong>model_fit_analysis/output/cs_results</strong></em> </p> <h2>4 - model_recovery</h2> <p>Contains code that execute model and parameter recovery analysis ('mp_recovery.R'), including HPC setup ('hpc/'). The 'mp_rec_analyse.R' reproduces model and parameter recovery results from the supplement.</p> <h2>5 - Figures</h2> <p>Contains all the figures from the manuscript and the supplement.</p> <h2>6 - RDS_fits</h2> <p>Contains RStan fit objects for each condition for each model</p>
Parallel dynamics of bacterial genome reduction across independent transitions to endosymbiosis.
<p>The establishment of symbiosis dramatically alters the evolution of the associated species, making symbiotic systems ideal models for studying the impact of lifestyle changes on genomes. Here, we focused on Enterobacterales, a large and ancient bacterial lineage that includes endosymbionts with diverse host associations, ranging from gut inhabitants to intracellular environments, and from horizontal to vertical transmission. Leveraging over two hundred genomes, along with cutting-edge single-copy gene concatenation and multi-copy gene family approaches, we inferred a robust phylogenetic framework that supports eleven independent transitions to endosymbiosis. Inferences on patterns of genome evolution confirm previous hypotheses about the processes underlying genome reduction: a substantial spike in gene loss always occurs simultaneously with the establishment of endosymbiosis, while a reduction in gene acquisition mechanisms is associated with the subsequent genome erosion. Furthermore, gene family loss frequencies were correlated across independent endosymbiotic clades; genes with more conserved functions and stronger constraints on sequence evolution are lost less frequently, suggesting that differences in gene essentiality and dispensability drive the observed parallelism. Our analyses contribute to the coming of age of the theory of genome evolution in symbiotic associations and provide novel insights into the importance of recombination as an opposing force against genome erosion.</p>
Are there two independent evaluative conditioning effects in relational paradigms? Dissociating the effects of CS-US pairings and their meaning
<p>Recent research into evaluative conditioning (EC) shows that information about the relationship between the conditioned and unconditioned stimuli can exert strong effects on the size and direction of the EC effect. Additionally, the co-occurrence of these stimuli seems to exert an orthogonal effect on evaluations. This finding has been interpreted as support for two independent types of EC effects. However, previous research devoted to this question relied on aggregated evaluative measures, allowing for alternative interpretations. In four experiments, we developed and validated a multinomial processing tree model that distinguishes effects of the pairings from effects of the meaning of the pairings. Our findings suggest that two independent EC effects contribute to overall evaluative change in a relational EC paradigm. The model that we developed offers a helpful method for future research in that it allows for an assessment of the effects of manipulations on processes rather than overall performance on an evaluative measure.</p>
Supplementary File S2: Plasmids for independently tunable, low-noise gene expression
<p>Supplementary File S2 README</p> <p>2019-April-26</p> <p>"Plasmids for independently tunable, low-noise gene expression" (Version 2)</p> <p>João P. N. Silva, Soraia Vidigal Lopes, Diogo J. Grilo, Zach Hensel</p> <p>This file describes the contents of the supplementary file for this manuscript. Python scripts were run in a Python 3 environment on OSX with various scientific python packages updated as of April 2019. With minor modifications for any similar environment it should be possible to generate Figures 1, 2, and 4 in the manuscript from these scripts and raw data.</p> <p>Contents:</p> <p>\dna sequences<br> \pDG101.gb Annotated DNA sequence in genbank format of plasmid pDG101<br> \pJS101.gb Annotated DNA sequence in genbank format of plasmid pJS101 (AddGene #118280)<br> \pJS102.gb Annotated DNA sequence in genbank format of plasmid pJS102 (AddGene #118281)<br> \pZH501.gb Annotated DNA sequence in genbank format of plasmid pZH501<br> \pZH509.gb Annotated DNA sequence in genbank format of plasmid pZH509 (AddGene #102664)<br> \pZH713.gb Annotated DNA sequence in genbank format of plasmid pZH713<br> \ZHX99.gb Annotated DNA sequence in genbank format for E. coli MG1655 chromosome insertion mutant ZHX99<br> <br> \data<br> \DG FCS Data: Raw flow cytometry data from BioRad S3 sorted by day and experimental condition; file name format: plasmid_inducer-concentration_inducer-units_inducer.fcs<br> \pJS101 pDG101 independence<br> \"quick scope intensity.ijm" Fiji macro used to extract average fluorescence intensities<br> \"Microscope Data\" Microscope data analyzed using the above Fiji macro; directory names indicate ATc and IPTG concentrations for each experimentation condition/replicate<br> \"intensity analysis\"<br> X_nM_ATc_Y_uM_IPTG.csv files: Exported CSV data from Fiji for each condition<br> backgrounds.csv: Average intensity for every condition, image frame, and color for background subtraction<br> \"images for Figure 4": Image stack with raw images used to generate Fig 4A and 4B</p> <p>\code<br> \fcsAnalysis_final_181228.py step-wise script for generating Figures 1 and 2 from FCS data<br> \fcsCalcDirectory181228.py script containing functions for FCS analysis and figure generation<br> \fcsImages PDF figures output by FCS analysis scripts<br> \FlowCal-master Distribution of the FlowCal library used in analysis for this manuscript; this is distributed under the MIT license<br> \scopeAnalysisWorkflow190430.py step-wise script for generating Figures 4C and 4D from cell fluorescence microscopy data in CSV format exported from Fiji<br> \scopeCalcDirectory190430.py script containing functions for microscopy data analysis and figure generation</p>
data set related to article Independent adaptation mechanisms for numerosity and size perception provide evidence against a common sense of magnitude
<p>This record contains raw data related to article Independent adaptation mechanisms for numerosity and size perception provide evidence against a common sense of magnitude</p>
Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome
<p>Mass spectrometry (MS)-based metaproteomics is used to identify and quantify proteins in microbiome samples, with the frequently used methodology being Data-Dependent Acquisition mass spectrometry (DDA-MS). However, DDA-MS is limited in its ability to reproducibly identify and quantify lower abundant peptides and proteins. To address DDA-MS deficiencies, proteomics researchers have started using Data-Independent Acquisition Mass Spectrometry (DIA-MS) for reproducible detection and quantification of peptides and proteins. We sought to evaluate the reproducibility and accuracy of DIA-MS metaproteomic measurements relative to DDA-MS metaproteomic measurements using a mock community of known taxonomic composition. Artificial microbial communities of known composition were analyzed independently in three laboratories using DDA- and DIA-MS acquisition methods. DIA-MS yielded more protein and peptide identifications than DDA-MS in each laboratory. In addition, the protein and peptide identifications were more reproducible in all laboratories and provided an accurate quantification of proteins and taxonomic groups in the samples. We also identified some limitations of current DIA tools when applied to metaproteomic data highlighting specific needs to further improve DIA tools to enable analysis of metaproteomic datasets from complex microbiomes. Ultimately, DIA-MS represents a promising data collection strategy for MS-based metaproteomics due to its large number of detected proteins and peptides, reproducibility, deep sequencing capabilities, and accurate quantitation.</p>
ScienceDex guides
Understand access before you commit
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.