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20 results for “Axial patterning”
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>
The ontogenetic pattern of neurocentral suture closure in the axial skeleton of Hyperodapedontinae (Archosauromorpha: Rhynchosauria) and its evolutionary implication
<p>Understanding ontogeny of a taxon is a crucial step to properly elucidate its taxonomy and evolution. However, aside from histological data, osteological criteria for assessing maturity are considered lineage specific or controversial. The sequence of neurocentral suture closure of the axial skeleton of extant crocodilians, which occurs in a postero-anterior sequence, has being used as a non-destructive method to determine maturity in extinct reptiles. However, the use of this criterion in extinct archosaurs not closely related to crocodilians is debatable, as the ancestral condition of Archosauria is unknown and variation occurs in timing and sequence orientation within the clade. We have assessed the pattern of neurocentral suture closure of the Hyperodapedontinae rhynchosaurs, an early archosauromorph clade distantly related to archosaurs. Different from extant crocodilians, they exhibit an antero-posterior sequence neurocentral suture closure. Relative size and other ontogenetic markers suggest the neurocentral closure in the Hyperodapedontinae is correlated to aging, although closed sutures were rare in the sample. A high number of open or partially open sutures in mature individuals indicate that they remained open during most of their life. Our study indicates that (i) the delayed neurocentral closure can be a paedomorphic heterochronic process in Hyperodapedontinae, as it contrasts with the fully closed neurocentral sutures of early diverging non-hyperodapedontine rhynchosaurs; (ii) the assumption opened neurocentral sutures indicates immaturity in extinct reptiles is not always correct; and (iii) the delayed closure may have originated independently in several archosauromorph lineages, but the ancestral condition of Archosauria likely follows the crocodilian closure pattern.</p>
Figure 5 in Evolution of axial patterning in elongate fishes
Figure 5. Number of abdominal and caudal vertebrae from our literature-based data set. Species were grouped into orders. Regression results are in Table 1, and a list of the species plotted is available in Supplementary Material: Table S1. The dotted line has a slope of one, indicating equal changes in abdominal and caudal vertebrae.
Figure 7 in Evolution of axial patterning in elongate fishes
Figure 7. Vertebral aspect ratio (AR) in the abdominal and caudal regions (AR = centrum length/centrum width). Solid lines are reduced major axis (RMA) regressions based on the raw data (the data points shown), and dashed lines are RMA regressions based on independent contrasts of abdominal and caudal aspect ratio. Regression statistics are given in Tables 4, 5.
Figure 3 in Evolution of axial patterning in elongate fishes
Figure 3. Intrarelationships of the seven groups included in our museum-based study. In the line drawings, the grey portion of each silhouette highlights the tail region of the body. A, Polypteriformes (Nelson, 1994); B, Osteoglossomorpha (Hilton, 2003); C, Elopomorpha (Belouze, 2002); D, Ostariophysi (Fink & Fink, 1981; Nelson, 1994); E, Paracanthopterygii (Patterson & Rosen, 1989; Endo, 2002); F, Beloniformes (Lovejoy, 2000); G, Scombroidei (Johnson & Baldwin, 1994).
Figure 2 in Evolution of axial patterning in elongate fishes
Figure 2. Models of axial patterning in fishes. A, vertebral number; B, vertebral aspect ratio (centrum length/centrum width). For an explanation of the models, see text.
Figure 1. Vertebrae from the Atlantic tarpon, Megalops atlanticus. A in Evolution of axial patterning in elongate fishes
Figure 1. Vertebrae from the Atlantic tarpon, Megalops atlanticus. A, anterior and lateral views of an abdominal vertebra with ribs; B, anterior and lateral views of a caudal vertebra with fused haemal arch.
Figure 4 in Evolution of axial patterning in elongate fishes
Figure 4. Contribution of increases in vertebral number and aspect ratio to overall body elongation. Elongation ratio (ER) is the standard length divided by the next largest body axis, either width or depth. The raw values plotted here were converted to independent contrast scores and a reduced major axis (RMA) regression, with the intercept forced through zero, was performed. A, total vertebral number vs. ER. Results from RMA regression on independent contrasts: y = 9.3x, R = 0.32, P = 0.02. B, vertebral aspect ratio (AR = centrum length/centrum width) vs. ER. Points represent the mean of abdominal and caudal ARs for each species. Results from RMA regression on independent contrasts: R = 0.18, P = 0.72. C, axial elongation index (AEI) vs. ER. AEI = (abdominal vertebral number)(abdominal AR) + (caudal vertebral number)(caudal AR). Results from RMA regression on independent contrasts: y = 10.0x, R = 0.46, P <0.001., Beloniformes;, Elopomorpha;, Ostariophysi;, Osteoglossomorpha;, Paracanthoptery-
Figure 9 in Evolution of axial patterning in elongate fishes
Figure 9. Squared-change parsimony traced phylogenies for abdominal aspect ratio and caudal aspect ratio. For each species, the mean of abdominal and caudal aspect ratio was calculated for this analysis. The interrelationships of the seven clades examined are based on Lauder & Liem (1983), and references for the intrarelationships are given in the legend to Fig. 3. Both traces are based on a squared-change parsimony algorithm in MacClade, version 4.06 (Maddison, 1991). Lighter coloured branches (white, yellow) are lower values of aspect ratio and darker branches (purple, black) are higher values of aspect ratio.
Figure 6 in Evolution of axial patterning in elongate fishes
Figure 6. Number of vertebrae in each of the two regions of the vertebral column, abdominal and caudal, for six clades in the museum-based study. Solid circles () represent the species means for number of abdominal vertebrae, and solid squares () represent the species means for number of caudal vertebrae. Solid regression lines are for abdominal vertebral number and dashed regression lines are for caudal vertebral number. The thick regression lines were calculated from the raw data points shown, and the thin regression lines are based on independent contrasts. Regression statistics are given in Tables 2, 3.
Figure 8 in Evolution of axial patterning in elongate fishes
Figure 8. Squared-change parsimony traced phylogenies for number of abdominal vertebrae and number of caudal vertebrae. The interrelationships of the seven clades examined are based on Lauder & Liem (1983), and references for the intrarelationships are given in the legend to Fig. 3. Both traces are based on a squared-change parsimony algorithm in MacClade, version 4.06 (Maddison, 1991). Lighter coloured branches (white, yellow) are lower vertebral numbers and darker branches (purple, black) are higher vertebral numbers. Electrophorus electricus was pseudocoloured in the number of caudal vertebrae to allow for greater resolution of the caudal vertebrae trace (see Material and methods). Two nodes are labelled A and B to allow their identification in the text.
The ontogenetic pattern of neurocentral suture closure in the axial skeleton of Hyperodapedontinae (Archosauromorpha: Rhynchosauria) and its evolutionary implication
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Nr6a1 controls axially-restricted body elongation, patterning and lineage allocation [dataset 2]
GEO Series GSE180426. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Axial skeleton anterior-posterior patterning is regulated through feedback regulation between Meis and retinoic acid
GEO Series GSE146301. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Nr6a1 controls axially-restricted body elongation, patterning and lineage allocation [dataset 1]
GEO Series GSE179858. Mus musculus. 30 samples. Type: Expression profiling by high throughput sequencing.
Polycomb-mediated axial patterning requires nucleosome compaction [ChIP-seq]
GEO Series GSE86084. Mus musculus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Polycomb-mediated axial patterning requires nucleosome compaction
GEO Series GSE86085. Mus musculus. 31 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Identification of direct transcriptional targets of BMP signaling during zebrafish dorsal-ventral axial patterning
GEO Series GSE163047. Danio rerio. 14 samples. Type: Expression profiling by high throughput sequencing.
Planarian yorkie/YAP functions to integrate adult stem cell proliferation, organ homeostasis, and maintenance of axial patterning
GEO Series GSE73700. Schmidtea mediterranea. 6 samples. Type: Expression profiling by high throughput sequencing.
Polycomb-mediated axial patterning requires nucleosome compaction [RNA-seq]
GEO Series GSE86083. Mus musculus. 27 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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International Brain Laboratory public data
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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.