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4,683 results for “embryonic”
ONT direct RNA sequencing Fast5 files from mouse embryonic stem cell (C57BL/6J x CAST/EiJ) - Rep1 (run1 and 4)
<p>We present a novel approach that leverages Oxford Nanopore direct RNA sequencing technology to detect allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNAs. Our approach utilized human and mouse cells with known genetic variants to ascertain allelic origin of each mRNA molecule. We employed a supervised machine learning model to detect read-level modification ratios, providing a comprehensive understanding of allele-specific m6A modification (ASM) patterns. To analyze the effects of allele specific m6A modification in mouse, we used hybrid mosue embryonic stem cells (C57BL/6J x CAST/EiJ). This page contains replicate 1 (run 1 and 4). </p>
ONT direct RNA sequencing Fast5 files from mouse embryonic stem cell (C57BL/6J x CAST/EiJ) - Rep2 (run3-2)
<p>We present a novel approach that leverages Oxford Nanopore direct RNA sequencing technology to detect allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNAs. Our approach utilized human and mouse cells with known genetic variants to ascertain allelic origin of each mRNA molecule. We employed a supervised machine learning model to detect read-level modification ratios, providing a comprehensive understanding of allele-specific m6A modification (ASM) patterns. To analyze the effects of allele specific m6A modification in mouse, we used hybrid mosue embryonic stem cells (C57BL/6J x CAST/EiJ). This page contains replicate 2 (run 3-2; the files are splited two two parts because of limitations of file size).</p>
ONT direct RNA sequencing Fast5 files from mouse embryonic stem cell (C57BL/6J x CAST/EiJ) - Rep2 (run4-2)
<p>We present a novel approach that leverages Oxford Nanopore direct RNA sequencing technology to detect allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNAs. Our approach utilized human and mouse cells with known genetic variants to ascertain allelic origin of each mRNA molecule. We employed a supervised machine learning model to detect read-level modification ratios, providing a comprehensive understanding of allele-specific m6A modification (ASM) patterns. To analyze the effects of allele specific m6A modification in mouse, we used hybrid mosue embryonic stem cells (C57BL/6J x CAST/EiJ). This page contains replicate 2 (run 4-2; the files are splited two two parts because of limitations of file size).</p>
ONT direct RNA sequencing Fast5 files from mouse embryonic stem cell (C57BL/6J x CAST/EiJ) - Rep2 (run4-1)
<p>We present a novel approach that leverages Oxford Nanopore direct RNA sequencing technology to detect allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNAs. Our approach utilized human and mouse cells with known genetic variants to ascertain allelic origin of each mRNA molecule. We employed a supervised machine learning model to detect read-level modification ratios, providing a comprehensive understanding of allele-specific m6A modification (ASM) patterns. To analyze the effects of allele specific m6A modification in mouse, we used hybrid mosue embryonic stem cells (C57BL/6J x CAST/EiJ). This page contains replicate 2 (run 4-1; the files are splited two two parts because of limitations of file size).</p>
Figure 11 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth
Figure 11. The egg tooth of Lacerta agilis at developmental stage 36. A, labiolingual histological section through the egg tooth and higher magnification of the area from the smaller box (inset), stained with H&E. B, labiolingual histological section through the egg tooth and dentin under higher magnification (inset) from the egg tooth tip, stained with AZAN trichrome. C, higher magnification of the area from the larger box in A showing a reversal line (arrows). D, transverse histological section through the anterior snout showing the cellular attachment tissue connecting the egg tooth to pleura, stained with H&E. E, sagittal cutaway of the snout (left), microtomographic sagittal (middle) and labiolingual (right) sections of the egg tooth. F, 3D reconstruction of the premaxilla and premaxillary teeth with exclusion of the egg tooth, ventral view. G, 3D reconstruction of the premaxilla and all premaxillary teeth, ventral view. H, 3D reconstruction of the premaxilla and the egg tooth (semi-transparent), right posterolateral view. Asterisks in E and F show the forming successor of the egg tooth. Scale bars: 100 μm.
Figure 4 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth
Figure 4. The egg tooth of Lacerta agilis at developmental stage 31. A, transverse histological section through the snout at the level of the egg tooth and forming premaxilla (asterisks), stained with H&E. B, 3D reconstruction of the palate. C, transverse histological section posterior to A, stained with H&E. D, transverse histological section posterior to C, stained with H&E. E, 3D reconstruction of the snout showing the egg tooth and forming premaxilla (asterisks), anterior semi-transparent view. F, microtomographic frontal section through the anterior snout. G, microtomographic frontal section through the anterior snout, ventral to F. Scale bars: 50 μm for histological sections; 500 μm for microtomographic sections.
Figure 7 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth
Figure 7. The premaxillary teeth of Lacerta agilis at developmental stage 34. A, labiolingual histological section through the egg tooth, stained with H&E. B, labiolingual histological section through the egg tooth, stained with AZAN trichrome. C, 3D reconstruction of the anterior snout, right lateral semi-transparent view. D, sagittal cutaway of the anterior snout. E, labiolingual histological section through the regular premaxillary tooth, stained with AZAN trichrome. F, labiolingual histological section through the regular premaxillary tooth, stained with H&E. Scale bars: 50 μm for histological sections; 200 μm for 3D reconstructions.
Figure 3 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth
Figure 3. The egg tooth of Lacerta agilis at developmental stage 29. A, transverse histological section through the snout at the level of the epithelial thickening of the forming egg tooth, stained with H&E. B, 3D reconstruction of the snout, lateroventral view. C, transverse histological section through the snout posterior to A, showing epithelial thickening of the forming regular premaxillary tooth (arrow). D, sagittal cutaway of the snout, stage 29, but slightly older than in A–C. E, 3D reconstruction of the snout, lateroventral semi-transparent view, stage 29, but slightly older than in A–C. F, transverse histological section through the snout at the level of the egg tooth bud (dotted line) stained with AZAN trichrome, stage 29, but slightly older than in D and E. G, transverse histological section through the snout at the level of the premaxillary dental lamina, stained with AZAN trichrome, posterior to F. Scale bars: 50 μm for histological sections; 500 μm for 3D reconstructions.
Figure 10 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth
Figure 10. The egg tooth of Lacerta agilis at developmental stage 36. A, stereomicroscope photomicrograph of the anterior snout, left ventrolateral view (mirrored). B, stereomicroscope photomicrograph of the anterior palate. C, 3D reconstruction of the snout, anterior view. D, scanning electron micrograph of the egg tooth showing a disruption of the enamel organ (arrow), ventral view. E, scanning electron micrograph of the lateral border of the egg tooth showing small bulges (arrowhead). F, scanning electron micrograph of the periderm cells covering the egg tooth. G, scanning electron micrograph of the microridges on the egg tooth periderm cells. Scale bars: 200 μm in A–D; 1 μm in E–G.
Figure 6 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth
Figure 6. The egg tooth of Lacerta agilis at developmental stage 34. A, stereomicroscope photomicrograph of the anterior palate. B, 3D reconstruction of the snout, anterior semi-transparent view. C, 3D reconstruction of the palate, anteroventral view. D, scanning electron micrograph of the anterior palate and the egg tooth surface (inset). Scale bars: 100 μm; 1 μm for inset in D.
Figure 2 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth
Figure 2. Transverse histological section through the snout of a Lacerta agilis embryo, stained with AZAN trichrome; developmental stage 28. A, section at the level of the facial prominence fusion (arrows). B, section at the level of the nasal plug, anterior to A. Scale bars: 50 μm.
Figure 5 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth
Figure 5. Transverse histological section through the snout of Lacerta agilis at developmental stage 32, stained with H&E. A, middle part of the developing egg tooth. B, anterior part of the developing egg tooth. C, posterior part of the developing egg tooth. D, premaxillary regular teeth at bud stage, section posterior to C. Scale bars: 50 μm; 25 μm for inset in B.
Figure 9 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth
Figure 9. The premaxillary teeth of Lacerta agilis at developmental stage 35. A, labiolingual histological section through the egg tooth showing the forming attachment tissue (asterisks), stained with AZAN trichrome. B, labiolingual histological section through the egg tooth showing the forming attachment tissue (asterisks), stained with H&E. C, 3D reconstruction of the palate, non-transparent (left) and semitransparent (right) view. D, sagittal cutaway of the anterior snout. E, labiolingual histological section through the regular premaxillary tooth and forming the subsequent premaxillary teeth (arrow), stained with AZAN trichrome. F, labiolingual histological section through the regular premaxillary teeth and primordium of the egg tooth successor (arrowhead), stained with H&E. Scale bars: 50 μm for histological sections; 100 μm for 3D reconstructions.
Figure 1 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth
Figure 1. Distribution of the egg tooth (teeth) and caruncle in amniotes. The snout drawings, except for Unidentata (based on this study), are based on the literature: Gekkota (Hermyt et al. 2020b), Sphenodon, turtle (Fioroni 1962), bird (Wang et al. 2017), crocodilian (García 2007), and monotreme (Fenelon et al. 2023). Silhouettes are from http://phylopic.org/. Note that this simplified phylogenetic tree assumes the existence of the molecular clades Unidentata (Burbrink et al. 2020) and Archelosauria (Crawford et al. 2015).
Figure 13 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth
Figure 13. The developmental sequences of the egg tooth, the most advanced regular premaxillary teeth, and the most advanced maxillary teeth.
Figure 12 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth
Figure 12. The premaxillary teeth of Lacerta agilis at developmental stage 36. A, 3D reconstruction of the anterior palate including semitransparent view (right). B, labiolingual histological section through the largest regular premaxillary tooth and higher magnification of the collagen fibres of the forming attachment tissue (asterisks in the inset), stained with AZAN trichrome. C, labiolingual histological section through the regular premaxillary teeth showing a reversal line (arrows) between the alveolar bone and premaxilla, stained with H&E. D, labiolingual histological section through the successor of the egg tooth, stained with AZAN trichrome. E, labiolingual histological section through the successor of the egg tooth, stained with H&E. F, transverse histological section through the snout at the level of maxillary and premaxillary dental laminae apposition, stained with H&E. Scale bars: 200 μm in A; 50 μm in B–F.
Figure 8 in Breaking through the eggshell: embryonic development of the premaxillary dentition in Lacerta agilis (Squamata: Unidentata) with special emphasis on the egg tooth
Figure 8. The egg tooth of Lacerta agilis at developmental stage 35. A, stereomicroscope photomicrograph of the anterior snout, left lateral view (mirrored), early developmental stage 35. B, stereomicroscope photomicrograph of the anterior snout, left lateral view (mirrored), at late developmental stage 35. C, stereomicroscope photomicrograph of the anterior palate, early developmental stage 35. D, stereomicroscope photomicrograph of the anterior palate, late developmental stage 35. E, scanning electron micrograph of the anterior palate, late developmental stage 35. F, magnification of the area from the box in E showing the egg tooth. G, magnification of the area from the box in F showing the small bulges (arrowheads) on the lateral border of the egg tooth. Scale bars: 200 μm in A–D; 50 μm in E, F; 5 μm in G.
Scale invariance in early embryonic development
<p>Data and analysis accompanying the paper:</p> <p>"Scale invariance in early embryonic development" </p> <p>Milos Nikolic, Victoria Antonetti, Feng Liu, Gentian Muhaxheri, Mariela D. Petkova, Martin Scheeler, Eric M. Smith, William Bialek and Thomas Gregor. </p> <p>arxiv.org/abs/2312.17684</p>
Human embryonic head scRNA-seq data
<p>These data contain scRNA-seq data of 50,059 single cells from the heads of five human embryos aged four to six weeks in Seurat object format. The data are the result of a re-analysis of primary scRNA-seq data from whole embryos (Xu et al., 2023 Nat. Cell Biol.; GEO accession number: GSE157329).</p> <p>The re-analysis is described in:</p> <p>Siewert, A., Hoeland, S., Mangold, E. <em>et al.</em> Combining genetic and single-cell expression data reveals cell types and novel candidate genes for orofacial clefting. <em>Sci Rep</em> <strong>14</strong>, 26492 (2024). https://doi.org/10.1038/s41598-024-77724-9</p> <div> <div> </div> </div>
Data from: Heterochronic shifts and conserved embryonic shape underlie crocodylian craniofacial disparity and convergence
The distinctive anatomy of the crocodylian skull is intimately linked with dietary ecology, resulting in repeated convergence on blunt- and slender-snouted ecomorphs. These evolutionary shifts depend upon modifications of the developmental processes which direct growth and morphogenesis. Here we examine the evolution of cranial ontogenetic trajectories to shed light on the mechanisms underlying convergent snout evolution. We use geometric morphometrics to quantify skeletogenesis in an evolutionary context and reconstruct ancestral patterns of ontogenetic allometry to understand the developmental drivers of craniofacial diversity within Crocodylia. Our analyses uncovered a conserved embryonic region of morphospace (CER) shared by all non-gavialid crocodylians regardless of their eventual adult ecomorph. This observation suggests the presence of conserved developmental processes during early development (before Ferguson stage 20) across most of Crocodylia. Ancestral state reconstruction of ontogenetic trajectories revealed heterochrony, developmental constraint, and developmental systems drift have all played essential roles in the evolution of ecomorphs. Based on these observations, we conclude that two separate, but interconnected, developmental programs controlling craniofacial morphogenesis and growth enabled the evolutionary plasticity of skull shape in crocodylians.
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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)
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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.