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Single-cell sequencing data of human umbilical cord and placental mesenchymal stem cells
<p>Expression matrix of umbilical cord and placenta single-cell sequencing data from the same donor.Table1 is the umbilical cord and Table2 is the placenta.</p>
AI4Life-MDC24 Challenge data: JUMP Cell Painting Datasets
<p>This is a subset of <em>the cpg0016-jump</em> dataset (<em>Chandrasekaran et al., 2022), available from the Cell Painting Gallery on the Registry of Open Data on AWS (<a href="https://registry.opendata.aws/cellpainting-gallery/" rel="nofollow">https://registry.opendata.aws/cellpainting-gallery/</a>). <br><br></em>The selected <strong>subset</strong> contains 517 images with four channels in the form of a single multi-channel tiff file. Gaussian noise is applied to each image to simulate the detector noise.</p> <p>The GitHub repository with the details about the original dataset is available at <a href="https://github.com/jump-cellpainting/datasets">https://github.com/jump-cellpainting/datasets</a>. The preprint describing the original dataset is <a href="https://www.biorxiv.org/content/10.1101/2023.03.23.534023v1">available on BioRxiv</a><br><br></p> <p>AI4Life has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement number 101057970. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.</p> <p> </p>
F I G U R E 1 3 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 1 3 Tyrosinase content of three kinds of loaches (*means P <0.05, **means P <0.01). () BBL; () SBL; () NBL; () dorsal skin; () abdominal skin
F I G U R E 3 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 3 The distribution of skin pigment cells in abdomen of three kinds of loaches. (a) The abdominal epidermis of big blackspot loaches (BBL), (b) the abdominal epidermis of small blackspot loaches (SBL) and (c) the abdominal epidermis of non-blackspot loaches (NBL). The blue arrow refers to xanthophores. The magnification (a–c) is 80
F I G U R E 9 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 9 Ultrathin sections of skin of three kinds of loaches. (a) The dorsal skin of big blackspot loaches (BBL), (b) the dorsal skin of small blackspot loaches (SBL), (c) the dorsal skin of non-blackspot loaches (NBL), (d) the abdominal skin of BBL, (e) the abdominal skin of SBL and (f) the abdominal skin of NBL; N refers to nucleus in the six figures (a–f); S refers to stratum corneum in the six figures (a–f); (g) the dorsal skin of BBL, (h) the dorsal skin of SBL, (i) the dorsal skin of NBL, (j) the abdominal skin of BBL, (k) the abdominal skin of SBL, (l) the abdominal skin of NBL. The magnification of (a–f) is 1500 and the magnification of (g–l) is 6000. The green arrow indicates stage 1; the yellow arrow indicates stage 2; the red arrow indicates stage 3; the black arrow indicates stage 4
F I G U R E 1 1 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 1 1 Lutein content of three kinds of loaches (*means P <0.05, **means P <0.01). () BBL; () SBL; () NBL; () dorsal skin; () abdominal skin
F I G U R E 2 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 2 Distribution of pigment cells on the dorsal epidermis of three kinds of loaches. (a) The dorsal epidermis of big blackspot loaches (BBL), (b) the dorsal epidermis of small blackspot loaches (SBL), (c) the dorsal epidermis of non-blackspot loaches (NBL), (d) the magnification of the dorsal epidermis melanocytes of BBL, (e) the magnification of the dorsal epidermis melanocytes of SBL and (f) the magnification of the dorsal epidermis melanocytes of NBL. The black arrow refers to the first type of melanocytes, and the red arrow refers to the second type of melanocytes. The blue arrow refers to xanthophores. The magnification of (a–c) is 80. The magnification of d is 200. The magnification of (e–f) is 400
F I G U R E 8 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 8 Iridophores in skin of three kinds of loaches. (a) The dorsal skin of big blackspot loaches (BBL), (b) the dorsal skin of small blackspot loaches (SBL), (c) the dorsal skin of non-blackspot loaches (NBL), (d) the abdominal skin of BBL, (e) the abdominal skin of SBL and (f) the abdominal skin of NBL. The black arrow indicates iridophores
F I G U R E 7 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 7 Melanocyte in skin of three kinds of loaches. (a) The dorsal skin of big blackspot loaches (BBL), (b) the dorsal skin of small blackspot loaches (SBL), (c) the dorsal skin of non-blackspot loaches (NBL), (d) the abdominal skin of BBL, (e) the abdominal skin of SBL and (f) the abdominal skin of NBL. The black arrow indicates melanocytes
F I G U R E 4 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 4 Skin microstructure of three kinds of loaches. (a) The dorsal skin of big blackspot loaches (BBL), (b) the dorsal skin of small blackspot loaches (SBL), (c) the dorsal skin of non-blackspot loaches (NBL), (d) the abdominal skin of BBL, (e) the abdominal skin of SBL and (f) the abdominal skin of NBL
F I G U R E 1 4 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 1 4 Tyrosinase activity in three kinds of loaches (*means P <0.05, **means P <0.01). () BBL; () SBL; () NBL; () serum; () dorsal skin; () abdominal skin
F I G U R E 1 2 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 1 2 The content of total carotenoids in three kinds of loaches (*means P <0.05, **means P <0.01). () BBL; () SBL; () NBL; () dorsal skin; () abdominal skin
F I G U R E 1 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 1 External morphology of big blackspot loaches (BBL), small blackspot loaches (SBL) and nonblackspot loaches (NBL). (a) The lateral side of BBL; (b) the lateral side of SBL; (c) the lateral side of NBL; (d) the dorsal side of BBL; (e) the dorsal side of SBL; (f) the dorsal side of NBL
F I G U R E 1 0 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 1 0 Melanin content of three kinds of loaches (*means P <0.05, **means P <0.01). () BBL; () SBL; () NBL; () dorsal skin; () abdominal skin
F I G U R E 6 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 6 Melanocyte distribution in skin of three kinds of loaches with MF staining. (a) The dorsal skin of big blackspot loaches (BBL), (b) the dorsal skin of small blackspot loaches (SBL), (c) the dorsal skin of non-blackspot loaches (NBL), (d) the abdominal skin of BBL, (e) the abdominal skin of SBL and (f) the abdominal skin of NBL. The black arrow indicates melanocytes
F I G U R E 5 in Analysis of pigment cell composition, pigment content, tyrosinase content and activity of three kinds of loaches Misgurnus anguillicaudatus from Poyang Lake
F I G U R E 5 Melanocytes distribution in skin of three kinds of loaches. (a) The dorsal skin of big blackspot loaches (BBL), (b) the dorsal skin of small blackspot loaches (SBL), (c) the dorsal skin of non-blackspot loaches (NBL), (d) the abdominal skin of BBL, (e) the abdominal skin of SBL and (f) the abdominal skin of NBL. The black arrow refers to melanocytes
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>
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.