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82 results for “Organogenesis”
Source data for Synthetic dynamic hydrogels promote degradation-independent in vitro organogenesis
<p>Source data and statistical analysis results for Synthetic dynamic hydrogels promote degradation-independent in vitro organogenesis</p>
Dataset: Organogenesis Holdings Inc. (ORGO) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
DAPI images, molecules and segmentation boundaries for: A Spatiotemporal Atlas of Mouse Gastrulation and Early Organogenesis to Explore Axial Patterning and Project In Vitro Models onto In Vivo Space
<div> </div> <p><strong>Data Description</strong></p> <ol> <li><strong>Stitched & rotated DAPI images</strong> - tiff file format filename indicates sample and optical z-slice position, i.e. embryo3_z5.tif is the DAPI image for embryo 3 in optical z-slice 5. Also provided in PNG format.</li> <li><strong>Detected molecules and cell segmentation in MoleculeExperiment objects</strong> - RDS files to read data using the MoleculeExperiment format in R/Bioconductor. Filename embryo3_z5.Rds indicates MoleculeExperiment RDS file for embryo 3 in optical z-slice 5. Coordinates are provided in microns. Note that z-slices 2 and 5 are only provided for embryos 1,2,3 as they were originally provided in Lohoff et al, Nature Biotechnology, 2023.</li> <li><strong>Pixels-to-microns conversion</strong> - pixelSize.R Simple R script/text to indicate the size of each pixel in the DAPI images, this is to align the coordinate systems between the DAPI images and molecules.<br><br> <div> <h4>Project Abstract</h4> </div> <p>At the onset of murine gastrulation, pluripotent epiblast cells migrate through the primitive streak, generating mesodermal and endodermal precursors, while the ectoderm arises from the remaining epiblast. Together, these germ layers establish the body plan, defining major body axes and initiating organogenesis. Although comprehensive single cell transcriptional atlases of dissociated mouse embryos across embryonic stages have provided valuable insights during gastrulation, the spatial context for cell differentiation and tissue patterning remain underexplored. In this study, we employed spatial transcriptomics to measure gene expression in mouse embryos at E6.5 and E7.5 and integrated these datasets with previously published E8.5 spatial transcriptomics and a scRNA-seq atlas spanning E6.5 to E9.5. This approach resulted in a comprehensive spatiotemporal atlas, comprising over 150,000 cells with 88 refined cell type annotations as well as genome-wide transcriptional imputation during mouse gastrulation and early organogenesis. The atlas facilitates exploration of gene expression dynamics along anterior-posterior and dorsal-ventral axes at cell type, tissue, and organismal scales, revealing insights into mesodermal fate decisions within the primitive streak. Moreover, we developed a bioinformatics pipeline to project additional scRNA-seq datasets into a spatiotemporal framework and demonstrate its utility by analysing cardiovascular models of gastrulation3. To maximise impact, the atlas is publicly accessible via a user-friendly web portal empowering the wider developmental and stem cell biology communities to explore mechanisms of early mouse development in a spatiotemporal context.</p> </li> </ol>
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis
Open the record for dataset details and reuse information.
Single-cell TCA cycle proteomics of human embryos during early organogenesis
Open the record for dataset details and reuse information.
FIGURE 25 in The floral organogenesis of Eurycorymbus cavaleriei (Sapindaceae) and its systematic implications
FIGURE 25. Diagrammatic representation of a partial cyme of Eurycorymbus cavaleriei. The order of sepal initiation is given by numbers. Size of the flowers corresponds with their respective age. B, bracts and bracteoles. Arrow shows the orientation of monosymmetry at a mid-developmental stage in the oldest flower. Main inflorescence axis shown by a large dot.
FIGURES 13–24 in The floral organogenesis of Eurycorymbus cavaleriei (Sapindaceae) and its systematic implications
FIGURES 13–24. Floral development of Eurycorymbus cavaleriei. Fig. 13. Sequential initiation of a second adaxial petal primordium. The other one is hidden between sepals 1–3. Fig. 14. A young flower showing sepals, petals, stamens and carpel primordia (see stars). Fig. 15. Almost simultaneous initiation of the five petals and eight stamen primordia. There is an overlap between the initiation of the two petals next to sepal five and the last two stamens (arrows). Figs. 16 & 17. Slightly older stages, stamen primordia overtake the two delayed petal primordia (arrows) in size. Fig. 18. Differentiation of central carpellary area. Fig. 19. Carpel primordia initiate on the floral apex (see stars). Figs. 20 & 21. Successive stages of stamen diferentiation and carpel growth. Carpels expand progressively around a central meristem and develop a trilete apical slit. Two petals remain smaller for a long time (see arrows). Note the difference in size of the different petals. Figs. 22. Older stages of stamen diferentiation and carpel growth, showing the hairs starting to appear on the ovary and two smaller petals (see arrows). Fig. 23. Preanthesis staminate flower, showing parts of long folded filaments (see arrows) and disk; the degenerated ovary remains hidden. Fig. 24. In pistillate flowers, the ovary bulges out and the stamen development is arrested. Abbreviations in the images, C, carpel; F, floral primodia; N, disk; O, ovary; P, petal; S, stamen; and Se, sepal. Scale bars Figs. 13 & 15–21=50 μm, Figs. 14 & 22=100 μm, Figs. 23 & 24=200 μm.
FIGURES 1–12 in The floral organogenesis of Eurycorymbus cavaleriei (Sapindaceae) and its systematic implications
FIGURES 1–12. Floral morphology and organogenesis of Eurycorymbus cavaleriei. Fig. 1. Longitudinal section of lateral shoot of inflorescence with three flowers at different developmental stages. Differentiation of petals visible in top flower. Fig. 2. Transverse section of a young flower showing the arrangement and position of all organs. Fig. 3. A pistillate flower, showing bulging ovary, closed slits and degenerated stamens. Fig. 4. Staminate flower with stamens removed showing the extent of development of the extrastaminal disk. Fig. 5. Mature staminate flower with expanded filaments and nectary disk. Fig. 6. Transverse section of ovary, showing axile placentation. Fig. 7. A mature pistillate flower partly dissected showing two parallel ovules per locule. Fig. 8. Transverse section of ovary, showing the development of one or two ovules and the degeneration of the other ones. Fig. 9. Inflorescence primordium with more than five bracts being initiated in a spiral sequence. Lateral shoots arise in the axil of the bracts (visible where bracts are removed). Fig. 10. View of two floral primodia; the topflower shows the initiation of three sepals. Fig. 11. Apical view of lateral shoot with three flowers; sepal initiation visible on the top flower. Fig. 12. Five sepals are initiated sequentially. The arrow points to the first petal. Abbreviations in the images, B, bract; F, floral primodium; N, disk; P, petal; and Se, sepal. Scale bars: Figs. 9–12=50 μm, Figs. 2, 6 & 8=200 μm, Figs. 1, 3–5 & 7=500 μm.
Dataset of research about Potential of Purwoceng Extract (Pimpinella pruatjan Molkenb.) as Anti-Nicotine Therapy against Viability, Spermatozoa Membrane Integrity, and Organogenesis
<p>The dataset included:</p> <p>1. Ethical test certificate</p> <p>2. Description of ethical clearance</p> <p>3. List of figures of tools and goods used for this study</p> <p>4. Result of active ingredient purwoceng test certificates</p> <p>5. Results of Observation of Viability and Integrity of Spermatozoa Membranes appendices</p>
Venom gland organogenesis in the common house spider
<p>This archive includes the R codes and data (i.e., kallisto pseudoalignments) to make the gene expression matrix and calculate the fold change. This was use to identify venom gland-specific genes which were used as markers. The file provided include:</p> <ul> <li>bulk_RNA-seq.zip: this folder contains the kallisto pseudoalignments and the genome annotation</li> <li>bulk_RNA-seq.Rmd: R markdown with the codes for the analysis</li> <li>bulk_RNA-seq.html: the knit from the R markdown</li> </ul> <p>In addition, this archive provides the images of the HCR experiments taken as z-stacks using a a Stellaris 5 White Light Laser (Leica Microsystems) inverted confocal microscope. Once unzipped the folder, the files can be opened using Fiji. The developmental stage and the HCR probe set are specified either in the file ot the images' names. There are two sets of multi-HCR experiments:</p> <ul> <li>set 1 includes: toxin (Alexa-488), <em>sum-1</em> (Alexa-647), and <em>Dll</em> (Alexa-594);</li> <li>set 2 included <em>sage</em> (Alexa-647) and <em>fkh</em> (Alexa-488).</li> </ul>
Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis
GEO Series GSE87038. Mus musculus. 32 samples. Type: Expression profiling by high throughput sequencing.
Identification of genes expressed in a mesenchymal subset regulating prostate organogenesis using tissue and single cell transcriptomics
GEO Series GSE103011. Rattus norvegicus. 119 samples. Type: Expression profiling by high throughput sequencing.
A YY1-dependent increase in aerobic metabolism is indispensable for intestinal organogenesis
GEO Series GSE85602. Mus musculus. 4 samples. Type: Expression profiling by array.
Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq-add]
GEO Series GSE277789. Mus musculus. 830 samples. Type: Expression profiling by high throughput sequencing.
TIP55, a splice isoform of the KAT5 acetyltransferase, is essential for developmental gene regulation and organogenesis
GEO Series GSE111691. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Adult hepatocytes direct liver organogenesis through non-parenchymal cell recruitment in the kidney
GEO Series GSE99141. Mus musculus. 15 samples. Type: Expression profiling by array.
TBX3 is dynamically expressed in pancreatic organogenesis and fine-tunes regeneration
GEO Series GSE216889. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
CPL4 is a suppressor of de novo shoot organogenesis from roots of Arabidopsis thaliana
GEO Series GSE104083. Arabidopsis thaliana. 12 samples. Type: Expression profiling by high throughput sequencing.
Self-organizing models of human trunk organogenesis recapitulate spinal cord and spine co-morphogenesis.
GEO Series GSE215983. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing; Other.
Adaptable durable human endothelial cells for organogenesis and tumorigenesis
GEO Series GSE131039. Mus musculus; Homo sapiens. 44 samples. Type: Expression profiling by high throughput sequencing.
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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.