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15,022 results for “differentiation”
SPATIAL DIFFERENTIATION OF THE EMISSIVITY OF AGRICULTURE IN EUROPE
<p>The file contains the data used in the article: <br>DOI:10.5604/01.3001.0054.4326</p> <p>Replacements included in the file (for 2020):<br>Country<br>Item: IPCC Agriculture<br>Total emissions in tonnes<br>Emissions per hectare of agricultural land<br>Emissions per unit value of goods produced by agriculture<br>Emissions per capita</p> <p><br>Source: FAOSTAT database</p>
Differential DNA methylation in the benign and cancerous prostate tissue of African American and European American men
<p>The data presented here are the summary statistics for the manuscript, "Differential DNA methylation in the benign and cancerous prostate tissue of African American and European American men." The study aims to improve our understanding of prostate cancer disparities between African American and European American men by comparing the DNA methylation features that distinguish tumor and paired, histologically benign tissue from a sample of African American and European American prostate cancer patients. The summary statistics presented here represent the results of a differential methylation analyses comparing tumor and benign tissue in each ancestry group as well as the results of an analysis of differential methylation by ancestry group within each tissue. </p> <p>The files included are: </p> <p>AA_TumorvBenign_Dummy.zip which contains the results of the association analysis between tumor vs benign (benign as the default) tissue status and individual CpG sites in African Americans based on a model that accounts for the paired nature of samples using a series of dummy variables for individual. </p> <p>AA_TumorvBenign_MixedModel.zip which which contains the results of the association analysis between tumor vs benign (benign as the default) tissue status and individual CpG sites in African Americans based on a model that accounts for the paired nature of samples using a linear mixed model that included patient as a random effect. </p> <p>EA_TumorvBenign_Dummy.zip which contains the results of the association analysis between tumor vs benign (benign as the default) tissue status and individual CpG sites in European Americans based on a model that accounts for the paired nature of samples using a series of dummy variables for individual. </p> <p>EA_TumorvBenign_MixedModel.zip which which contains the results of the association analysis between tumor vs benign (benign as the default) tissue status and individual CpG sites in European Americans based on a model that accounts for the paired nature of samples using a linear mixed model that included patient as a random effect. </p> <p>Benign_AncestryCompare_Summary.zip which contains the results of an association analysis between ancestry designation (African American vs European American with African American as the baseline) and individual CpG sites in benign tissue. </p> <p>Tumor_AncestryCompare_Summary.zip which contains the results of an association analysis between ancestry designation (African American vs European American with African American as the baseline) and individual CpG sites in tumore tissue. </p>
Sensitivity maps of the Amundsen Sea Embayment to changes in external forcings using Automatic Differentiation
<p>Sensitivity maps of the final volume above flotation after 20 years to the basal friction coefficient, rheology factor, surface mass balance, and ocean-induced melting. These results were computed from STREAMICE and ISSM using automatic differentiation. See manuscript for complete description</p>
Data for: Polystyrene nanoplastics differentially influence the outcome of infection by two microparasites of the host Daphnia magna
<p>This dataset supports the findings of the study 'Polystyrene nanoplastics differentially influence the outcome of infection by two microparasites of the host <em>Daphnia magna</em>', published in Philosophical Transactions of the Royal Society B (https://doi.org/10.1098/rstb.2022.0013).</p>
Non-genetically-based intraspecific differentiation for heavy metal tolerance in the copper moss Scopelophila cataractae
<p>We used next-generation sequencing to study DNA methylation and gene expression changes in plants from four clonal populations of the metallophyte moss <em>Scopelophila cataractae</em> experimentally exposed to either Cd or Cu. For this we performed reduced representation bisulfite DNA sequencing and RNA sequencing. </p>
Even short‐distance dispersal over a barrier can affect genetic differentiation in Gyraulus, an island freshwater snail
<p>Supplementary dataset for a published paper, "Saito T., Sasaki T., Tsunamoto Y., Uchida S., Satake K., Suyama Y., <em>et al.</em> (2022). Even short‐distance dispersal over a barrier can affect genetic differentiation in <em>Gyraulus</em> , an island freshwater snail. <em>Freshwater Biology</em> <strong>67</strong>, 1971–1983. <a href="https://doi.org/10.1111/fwb.13990">https://doi.org/10.1111/fwb.13990</a>"</p>
Insights into metabolic changes during epidermal differentiation as revealed by multiphoton microscopy with fluorescence lifetime imaging
<p>Rapid developments in the field of organotypic cultures has generated a growing need for effective quality control measures during tissue development. In this study, we correlate metabolic changes with epidermal differentiation and demonstrate that multiphoton microscopy with fluorescence lifetime imaging (MPM-FLIM) can be applied as a non-invasive approach to monitor epidermal differentiation of keratinocytes with respect to proliferative and differentiated states. Keratinocytes grown at 1.5 mM Ca2+ exhibited increased expression of differentiation markers KRT1 and KRT10 compared to 60 μM Ca2+, and a metabolic shift from glycolysis to mitochondrial respiration. Fitting the fluorescence decay with a biexponential model revealed a decreased relative fraction of intracellular NADH and FAD after high calcium treatment, consistent with increased oxidative phosphorylation. Using these two parameters, the epidermal differentiation process could be monitored over a 96 h period. Implementing discriminating analysis based on k-means clustering generated clusters that correlated well with culturing time, suggesting that this methodology can be employed as part of an automated pipeline for monitoring keratinocyte differentiation.</p>
Differential Interferogram of the September 16 2018 Mw 5.3 earthquake Lake Muir, Perth, Australia
<p>A moderate earthquake of Mw 5.3 (M<sub>L</sub> 5.7) occured on September 16 2018 near the Lake Muir region, Perth, SW Australia. Despite Australia being in a mostly stable continental interior, moderate or strong shallow crustral earthquakes occured the past years. Due to shallow faulting and low relief/semi-arid conditions in most regions of Australia, even moderate events lead to surficial deformation in form of mapped surface ruptures or deformation identified by radar satellites (InSAR).</p> <p>The Sep.16 earthquake produced a distinctive surficial deformation pattern, identified in an interferometric pair of Sentinel-1 Copernicus radar images (Descending orbit, September 14 - September 26). Sentinel-1 TOPS Interferogram and Line-of-Sight (LOS) displacement were produced using SNAP and DIAPASON tools in the <a href="https://geohazards-tep.eo.esa.int">Geohazards Exploitation Platform</a>. Color fringes on interferogram represent each a ~2.8cm displacement. Displacement (unwrapped) grid files are also provided.</p> <p>InSAR analysis show co-seismic rupture along a NNE-SSW reverse fault plane, consistent with published moment tensors (USGS). LOS profiles show a 5-15cm displacement across a fault rupture that propagated to the surface. Hundreds of metres of fractures and surface ruptures were reported by local farmers' accounts and photographs to the ABC South West Australia news agency.</p>
Meta-analysis results of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight
<p>Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from -183 to 178 grams per 10% increase in methylation (P<sub>Bonferroni</sub><1.06x10<sup>-7</sup>).</p>
LRRK2 G2019S mutation suppresses differentiation of Th9 and Treg cells via JAK/STAT3
<p>Flow cytometry (Immune profiling) Tidy Data: Figure 1d,e, 2d</p> <p>ELISA Tidy Data: Figure 2c, 4b</p> <p>qRT-PCR Tidy Data: Figure 1b, 3a, 4c,d</p> <p>Cell count Tidy Data: Figure 2b</p> <p> </p> <p> </p>
Accelerating Quantum Emitter Characterization with Latent Neural Ordinary Differential Equations
<p>Datasets used in 'Accelerating Quantum Emitter Characterization with Latent Neural Ordinary Differential Equations', published in AI4Mat-NeurIPS-2024.</p> <ul> <li>pcfs_g2_2d_n50000_20240623_nstage200_maxdelay66_.h5 was used for inputs and predictions in Fig. 1 and Fig. 2</li> <li>pcfs_g2_2d_n50000_20240820_nstage100_maxdelay120.h5 was used for inputs and predictions in Fig. 3</li> </ul> <p> </p>
xPore: Identification of differential RNA modifications from nanopore direct RNA sequencing - SGNEx data
<p>xPore is a Python package for identification and quantification of differential RNA modifications from direct RNA sequencing.</p> <p>The detailed usage is documented at <a href="https://xpore.readthedocs.io/en/latest/">https://xpore.readthedocs.io/en/latest</a>, while all scripts and source code are available at <a href="https://github.com/GoekeLab/xpore">https://github.com/GoekeLab/xpore</a>.</p> <p>All the preprocessed datasets used in the paper are provided here. </p> <p>Please cite our paper below when using these data.<br> Ploy N. Pratanwanich et al. "Detection of differential RNA modifications from direct RNA sequencing of human cell lines." bioRxiv (2020).</p>
Chromatin activity identifies differential gene regulation across human ancestries
<p>This repository contains data related to:</p> <p>Chromatin activity identifies differential gene regulation across human ancestries</p> <p>Kade P. Pettie, Maxwell Mumbach, Amanda J. Lea, Julien Ayroles, Howard Y. Chang, Maya Kasowski, Hunter B. Fraser</p> <p> </p>
The Vibrio Type III Secretion System 2 is not restricted to the Vibrionaceae and encodes differentially distributed repertoires of effector proteins
<p>Supplementary Dataset for the work entitled "The Vibrio Type III Secretion System 2 is not restricted to the Vibrionaceae and encodes differentially distributed repertoires of effector proteins".</p> <p>This dataset includes files for the T3SS2 reconstructed phylogenetic tree (Newick tree and fasta file), hierarchical clustering data analysis file from MORPHEUS, Table S1 with genome accession numbers, and all the data of the absence/presence of T3SS2-related components, Table S2 with the prediction of novel effector proteins.</p>
Reproduction package for the paper "Measuring the variability of directly imaged exoplanets using vector Apodizing Phase Plates combined with ground-based differential spectrophotometry"
<p>This is a basic reproduction package for the paper <a href="https://doi.org/10.1093/mnras/stad249">"Measuring the variability of directly imaged exoplanets using vector Apodizing Phase Plates combined with ground-based differential spectrophotometry" by Sutlieff et al. (2023)</a>. It aims to provide the most important data products to check and reproduce the main results of the paper.</p>
Differential response of α-synuclein expression to bacterial ligands and metabolites in mouse enteroendocrine cells
<p>Dataset for manuscript <em>"<strong> </strong></em><strong>α</strong><strong>-synuclein expression in response to bacterial ligands and metabolites in gut enteroendocrine cells</strong><em>". </em>Tabs in excel file are title with the figure number. </p>
Single-Cell Profiling of CD8+ T Cells in Acute Myeloid Leukemia Reveals a Continuous Spectrum of Differentiation and Clonal Hyperexpansion
<p>Data for the publication <strong>Single-Cell Profiling of CD8<sup>+</sup> T Cells in Acute Myeloid Leukemia Reveals a Continuous Spectrum of Differentiation and Clonal Hyperexpansion</strong></p>
Datasets, reproducible codes, and results for evaluating differential expression analysis methods on population-level RNA-seq data
<p>This upload contains the necessary R codes and data to reproduce the FDR and Power results described in our correspondence "Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives" to Li Y, Ge X, Peng F, Li W, Li JJ, Exaggerated false positives by popular differential expression methods when analyzing human population samples, <em>Genome Biology</em> 23, 79, 2022, DOI: 10.1186/s13059-022-02648-4.</p>
A Linked Application of Discrete Differential Evolution Algorithm Coupled with Simulation- Optimization Model and Comparative Analysis by Genetic Algorithm for Discrete Groundwater Management Problems
<p>Complete dataset of publication name as "The complete publication dataset is "A Discrete Differential Evolution- Linear Programming Algorithm for Groundwater Management Problems." You can find all the written codes in the zip file.</p>
RNA-Seq data from: Hox genes modulate physical forces to differentially shape small and large intestinal epithelia
<p>Hox genes are highly conserved, master regulators of spatial patterning in the embryo, but how these factors trigger regional morphogenesis has largely remained a mystery. In the developing gut, Hox genes help demarcate identities of the small and large intestines early in embryogenesis, which ultimately leads to their specialization in both form and function. While the midgut forms villi, the hindgut develops flat, brain-like sulci that resolve into heterogeneous outgrowths. Combining mechanical measurements and mathematical modeling, we demonstrate that the posterior Hox gene Hoxd13 regulates biophysical phenomena that shape the hindgut lumen. We further show that Hoxd13 acts through the TGFβ pathway to thicken, stiffen, and promote isotropic growth of the subepithelial mesenchyme; together, these features lead to hindgut surface buckling. TGFβ, in turn, promotes collagen deposition to affect mesenchymal geometry and growth. We thus identify a cascade of events downstream of positional genetic identity that direct posterior intestinal morphogenesis. </p> <p>To identify genes and pathways that are directly or indirectly regulated by Hoxd13 to affect posterior gut morphogenesis in the chick, we compared mesodermal transcriptomes of wild-type midgut and hindgut intestinal samples, as well as mesodermal samples from a Hoxd13-overexpressing midgut at E12 and E14. Tissues were dissected and endoderm layers were removed manually before RNA extraction and downstream processing. Unbiased clustering was used to identify genes commonly differentially expressed in the hindgut and Hoxd13-misexpressing midgut. This submission contains bulk RNA-seq raw data (fastq.bz2 files) and processed .txt files with read counts. Experiment information is provided in .xlsx Metadata file used for NCBI GEO submission.</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.