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56 results for “Source data for figures”
Tuning apicobasal polarity and junctional recycling in the hemogenic endothelium orchestrates the morphodynamic complexity of emerging pre-hematopoietic stem cells —Source data 4 relative to Figure 7 – ArhGEF11 CRISPR interference
<p><span>Raw image files (TIFF format), corresponding 2D-cartographies (_2Dmap.tiff files) and metadata files for 2D-cartographies (.xml files, readable with the opensource software Icy), relative to <strong>Figure 7B </strong>and<strong> Figure 7 - Figure Supplement 6</strong> (see <strong>Materials and Methods — Morphological and morphometric analysis of aortic and hemogenic cells</strong>).</span></p> <p><span>The source data comprises for each 48 - 55 hpf <em>Tg(kdrl:eGFP-JAM3b; kdrl:nls-mKate2)</em> zebrafish embryo 3 z-stack and 2D cartographies (segments 1 to 3) encompassing the whole length of the aorta, for control condition (n = 2 individuals) and morpholino splicing interference condition (n = 2 individuals). For z-stacks of both control and morphant conditions, two fluorescence channels were acquired, corresponding to the nuclear mKate2 expressed in endothelial cells and the eGFP-JAMs signal localized at the intercellular junctions of endothelial cells. Z-stack were acquired using a confocal spinning disk microscope. Voxel size: x: 0.1635, y: 0.1635, z:0.3 µm. 2D-cartographies were obtained using the Icy plugin “TubeSkinner”, and the semi-manual segmentation of all aortic cells can be uploaded from the corresponding metadata file on the 2D-cartographies using the load ROI function of Icy.</span></p>
Tuning apicobasal polarity and junctional recycling in the hemogenic endothelium orchestrates the morphodynamic complexity of emerging pre-hematopoietic stem cells —Source data 3 relative to Figure 7 – ArhGEF11 morpholino splicing interference
<p><span>Raw image files (TIFF format), corresponding 2D-cartographies (_2Dmap.tiff files) and metadata files for 2D-cartographies (.xml files, readable with the opensource software Icy), relative to <strong>Figure 7A </strong>and<strong> Figure 7 - Figure Supplement 5</strong> (see <strong>Materials and Methods — Morphological and morphometric analysis of aortic and hemogenic cells</strong>).</span></p> <p><span>The source data comprises for each 48 - 55 hpf <em>Tg(kdrl:eGFP-JAM2a; kdrl:nls-mKate2)</em> zebrafish embryo 3 z-stack and 2D cartographies (segments 1 to 3) encompassing the whole length of the aorta, for control condition (n = 2 individuals) and morpholino splicing interference condition (n = 3 individuals). For z-stacks of both control and morphant conditions, two fluorescence channels were acquired, corresponding to the nuclear mKate2 expressed in endothelial cells and the eGFP-JAMs signal localized at the intercellular junctions of endothelial cells. Z-stack were acquired using a confocal spinning disk microscope. Voxel size: x: 0.1635, y: 0.1635, z:0.3 µm. 2D-cartographies were obtained using the Icy plugin “TubeSkinner”, and the semi-manual segmentation of all aortic cells can be uploaded from the corresponding metadata file on the 2D-cartographies using the load ROI function of Icy.</span></p>
Tuning apicobasal polarity and junctional recycling in the hemogenic endothelium orchestrates the morphodynamic complexity of emerging pre-hematopoietic stem cells —Source data 1 relative to Figure 3
<p><span>Raw image files (TIFF format) relative <strong>to Figure 3</strong> (see <strong>Materials and Methods — Dt-runx1 phenotype analysis – cell count</strong>).</span></p> <p><span>The source data comprises for each 52 - 55 hpf zebrafish embryo 3 z-stack (segments 1 to 3) encompassing the whole length of the aorta, for control condition (<em>Tg(Kdrl:Gal4;UAS:RFP), </em>n = 3 individuals) and mutant condition (<em>Tg(kdrl:Gal4;UAS:RFP;4xNR:dt-runx1-eGFP), </em>n = 7 individuals). For control condition, one fluorescence channel was acquired, corresponding to the cytoplasmic RFP expressed in endothelial cells. For mutant condition, two fluorescence channels were acquired, corresponding first to the cytoplasmic RFP expressed in endothelial cells using the same reporter as for the control condition, and second the cleaved cytoplasmic GFP reporting the expression of our dt-runx1 mutant construct in endothelial cells. Z-stack were acquired using a confocal spinning disk microscope. Voxel size: x: 0.1635, y: 0.1635, z:0.3 µm.</span></p>
Tuning apicobasal polarity and junctional recycling in the hemogenic endothelium orchestrates the morphodynamic complexity of emerging pre-hematopoietic stem cells —Source data 2 relative to Figure 4
<p><span>Raw image files (TIFF format) and segmented 3D images (.ims, Imaris proprietary files) relative to <strong>Figure 4</strong> and <strong>Figure 4 Figure Supplement 3</strong> (see <strong>Materials and Methods — RNAscope image analysis – Pard3</strong>).</span></p> <p><span>The source data comprises for each 52 - 55 hpf zebrafish embryos 2 z-stack (segments 1 to 2) encompassing the whole length of the aorta, for control condition (<em>Tg(Kdrl:eGFP), </em>n = 7 individuals) and mutant condition (<em>Tg(kdrl:Gal4; 4xNR:dt-runx1-eGFP), </em>n = 12 individuals). For both control and mutant conditions, two fluorescence channels are displayed, corresponding to the cytoplasmic GFP expressed in endothelial cells (in green) and the RNAscope signal (OPAL-570, in magenta). Z-stack were acquired using a confocal spinning disk microscope. Voxel size: x: 0.1635, y: 0.1635, z:0.4 µm. The .ims files contain the 3D rendering of the z-stacks as well as the segmentations of Pard3ba mRNA RNAscope spots (in magenta), in the aorta (Spots 1 Selection) or outside (Spots 1), as well as the segmentation of endothelial cells (green) (Cells 1) and hemogenic endothelial cells (Cells 1 Cell export).</span></p>
Source data to create the figures of the study "Rising greenhouse gas emissions embodied in the global bioeconomy supply chain" using REX3 with new GHG extension including LULUCF
<p>This repository contains the source data to create the figures of the study <a href="https://doi.org/10.1038/s43247-025-02144-0">Rising greenhouse gas emissions embodied in the global bioeconomy supply chain</a> published in <em>Communications Earth & Environment</em>. The results were calculated with the REX3 database in Version 3.2 of this repository and the GHG extension and matlab codes in Version 3.4 of this repository.</p> <p>Figure 1, and 3–5 were created in Rstudio with the attached Rcode <em>Bioeconomy_GHG_sankeys.R</em></p> <p>Figure 2 was created in tableau with an <a href="https://public.tableau.com/app/profile/livia.cabernard/vizzes">interactive data visualizer</a> that allows to zoom into the global bioeconomy supply chain.</p>
Source Data for main text and supplemental figures for manuscript "Community assessment of methods to deconvolve cellular composition from bulk gene expression"
<p>Source Data for main text and supplemental figures for manuscript "Community assessment of methods to deconvolve cellular composition from bulk gene expression"</p>
Dense vegetation hinders sediment transport towards saltmarsh interiors - Supporting data and source code (Part V: Figures)
<p>This is Part V of the supporting data and source code for the paper entitled "Dense vegetation hinders sediment transport towards saltmarsh interiors", submitted to <em>Limnology and Oceanography Letters.</em> It contains all input and output files to generate the figures of the paper.</p> <p>To be able to run the scripts as is, the path (at the beginning of each script) to the following folders must be updated:</p> <p>Runs (includes all model run folders from Part II and Part III)<br>Post (includes all post-processing folders from Part IV)</p>
Source data: FtsK is critical for the assembly of the unique divisome complex of the FtsZ-less Chlamydia trachomatis figures 1-7
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Anonymized source data files for figures in: Recurrent processes support a cascade of hierarchical decisions
<p>Perception depends on a complex interplay between feedforward and recurrent processing. Yet, while the former has been extensively characterized, the computational organization of the latter remains largely unknown. Here, we use magneto-encephalography to localize, track and decode the feedforward and recurrent processes of reading, as elicited by letters and digits whose level of ambiguity was parametrically manipulated. We first confirm that a feedforward response propagates through the ventral and dorsal pathways within the first 200 ms. The subsequent activity is distributed across temporal, parietal and prefrontal cortices, which sequentially generate five levels of representations culminating in action-specific motor signals. Our decoding analyses reveal that both the content and the timing of these brain responses are best explained by a hierarchy of recurrent neural assemblies, which both maintain and broadcast increasingly rich representations. Together, these results show how recurrent processes generate, over extended time periods, a cascade of decisions that ultimately accounts for subjects' perceptual reports and reaction times.</p>
Figure 1. from Extending Marine Species Distribution Maps Using Non-Traditional Sources - Biodiversity Data Journal 3: e4900 (17 April 2015) https://doi.org/10.3897/BDJ.3.e4900
Figure 1. - The IUCN Red List Review Process (IUCN 2014a). Steps refer to the DOCUMENTATION STANDARDS AND CONSISTENCY CHECKS FOR IUCN RED LIST ASSESSMENTS AND SPECIES ACCOUNTS (IUCN 2013).
Figures and data for the paper Perceptual Evaluation of Source Separation for Remixing Music
<p>Listening test results and figures for the paper:</p> <p>H. Wierstorf, D. Ward, R. Mason, E. M. Grais, C. Hummersone, M. D. Plumbley,<br> "Perceptual Evaluation of Source Separation for Remixing Music," in 143rd<br> Convention of the Audio Engineering Society, 2017.</p> <p>`fig02/data/` contains the results from single listeners and median results across<br> listeners.<br> `fig02/fig02.plt` is the code to regenerate `fig02/fig02.pdf`.</p> <p>`fig03/data/` contains average medians across all songs.<br> `fig03/fig03.plt` is the code to regenerate `fig03/fig03.pdf`.</p> <p>The listening test results were extracted from the raw data stored together with<br> the experimental procedure in https://doi.org/10.5281/zenodo.835191.<br> There the file `experiment/saves/ratings/analyze_results.py` can be run in order<br> to regenerate the result files provided with this publication.<br> </p>
Source data for: All figures and tables included in NCOMMS-23-03997A
<p>Tools enable animals to exploit and command new resources. However, the neural circuits underpinning tool use and how neural activity varies with an animal's tool proficiency, are only known for humans and some other primates. We use 18F-fluorodeoxyglucose positron emission tomography to image the brain activity of naïve vs trained American crows (<em>Corvus brachyrhynchos</em>) when presented with a task requiring the use of stone tools. As in humans, talent affects the neural circuits activated by crows as they prepare to execute the task. Naïve and less proficient crows use neural circuits associated with sensory- and higher-order processing centers (the mesopallium and nidopallium), while highly proficient individuals increase activity in circuits associated with motor learning and tactile control (hippocampus, tegmentum, nucleus basorostralis, and cerebellum). Greater proficiency is found primarily in adult female crows and may reflect their need to use more cognitively complex strategies, like tool use, to obtain food.</p>
Source Data for all Figures
<p>Underlying data of Figures in paper "Efficient Scaling of Large Language Models with Mixture of Experts and 3D Analog In-Memory Computing" authored by Büchel et al.</p>
Vesicles clustering around Wdr35-/- cilia lack electron dense decorations although electron-dense clathrin coated vesicles are still observed budding from the mutant plasma membrane (Figure 7- source data 1)
<p>Intraflagellar transport (IFT) is a highly conserved mechanism for motor-driven transport of cargo within cilia, but how this cargo is selectively transported to cilia is unclear. WDR35/IFT121 is a component of the IFT-A complex best known for its role in ciliary retrograde transport. In the absence of WDR35, small mutant cilia form but fail to enrich in diverse classes of ciliary membrane proteins. In <i>Wdr35 </i>mouse mutants, the non-core IFT-A components are degraded and core components accumulate at the ciliary base. We reveal deep sequence homology of WDR35 and other IFT-A subunits to α and ß' COPI coatomer subunits, and demonstrate an accumulation of 'coat-less' vesicles which fail to fuse with <i>Wdr35 </i>mutant cilia. We determine that recombinant non-core IFT-As can bind directly to<u> </u>lipids and provide the first <i>in-situ</i> evidence of a novel coat function for WDR35, likely with other IFT-A proteins, in delivering ciliary membrane cargo necessary for cilia elongation.</p>
April 7, 2024 (v1) Image Open Tuning apicobasal polarity and junctional recycling in the hemogenic endothelium orchestrates the morphodynamic complexity of emerging pre-hematopoietic stem cells —Source data 5 relative to Figure 7 - Figure Supplement 4
<p>Source data file relative to <strong><span>Figure 7 – figure supplement 4 Panel A</span></strong></p> <p><span>Raw image of agarose gel showing the 2 alternative mRNAs encoding for ArhGEF11 in control animals (left track, control) and after injection of the MO at the one cell stage (right track, +MO at 2 and 5ng). The source data includes the raw files (native format .scn and open source format .tiff) as well as a pdf file showing both the full scale image and the cropped image selected for the figure.<br></span></p>
source data figures De Vries 2024 (Comm. E&E)
<p>This is the source data for producing the manuscript figures of De Vries et al. (2024) Comm. Earth & Env.</p>
Source Data Images for Figures 3a-d, Fig 4
<p>Source Data Files for Figures 3a-d, 4d</p> <p><strong>STAT5B<sup>N642H</sup> transforms T-cell subsets, resulting in differential peripheral organ infiltration.</strong></p> <p>Histological analysis using CD3, Ki67 and H&E staining of the skin, lung, liver and brain of 7- to 9-week-old wild type (WT), human STAT5B and human STAT5B<sup>N642H</sup> mice. Images are representative of three independent experiments. Original magnification: 4x (left panels in C and D), 20× and 40× (insets), scale bars = 100 μm. These images represent Source Data files for Figures 3a-d and 4d.</p> <p>Histological analysis using CD3, Ki67 and H&E staining of the liver of recipient mice transplanted with γδ T-cells from hSTAT5B<sup>N642H</sup> (n = 2) or WT (n = 1) mice. Original magnification: 20× and 40× (insets), scale bars = 100 μm.</p>
Figure source data for Riddell-Young et al., 2024 "Abrupt changes in biomass burning during the last glacial period"
<p>These are the source data files for all of the data presented in main text figures 1 through 4 in Riddell-Young et al., 2024: "Abrupt changes in biomass burning during the last glacial period". Each file contains several sheets that correspond to the data presented in each subplot of the figure. Please refer to the manuscript for a detailed description of the data that was collected and analysis that was performed as part of the study. The Data and Code Availability statements discuss where the official dataset and code publications can be found.</p>
Source data figures Diverse Slip behaviour on Velocity-Weakening fault segments
<p>txt data files for figures 3, 4 and 5 displayed on manuscript Diverse Slip behaviour on Velocity-Weakening fault segments</p>
Anonymized source data files for figures in: Recurrent processes support a cascade of hierarchical decisions
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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.