Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
23
datasets available to search
ShareScore release 0.9.0
Dataset results
23 results for “Invagination”
Figures and videos for: Patterned invagination prevents mechanical instability during gastrulation
<p>This repository contains the high-resolution figures and videos for the paper:</p> <p>Vellutini, B. C., Cuenca, M. B., Krishna, A., Szałapak, A., Modes, C. D. & Tomancak, P. Patterned invagination prevents mechanical instability during gastrulation. <em>Nature</em> (2025). doi:<a href="https://10.0.4.14/s41586-025-09480-3">10.1038/s41586-025-09480-3</a></p> <p>Please refer to the main repository for more information: <a href="https://doi.org/10.5281/zenodo.7781947">https://doi.org/10.5281/zenodo.7781947</a></p>
Repository for: Patterned invagination prevents mechanical instability during gastrulation
<p>This is the repository for the paper:</p> <p>Vellutini, B. C., Cuenca, M. B., Krishna, A., Szałapak, A., Modes, C. D. & Tomancak, P. Patterned invagination prevents mechanical instability during gastrulation. <em>Nature</em> (2025). doi:<a href="https://10.1038/s41586-025-09480-3">10.1038/s41586-025-09480-3</a></p> <p>Here are all the associated repositories:</p> <ul> <li><strong>Main repository (code and data):</strong> <a href="https://doi.org/10.5281/zenodo.7781947">https://doi.org/10.5281/zenodo.7781947</a></li> <li><strong>Model and simulations (code and data):</strong> <a href="https://doi.org/10.5281/zenodo.7784906">https://doi.org/10.5281/zenodo.7784906</a></li> <li><strong>Lightsheet and in situ experiments (imaging data):</strong> <a href="https://doi.org/10.5281/zenodo.15876638">https://doi.org/10.5281/zenodo.15876638</a></li> <li><strong>Laser perturbation experiments (imaging data):</strong> <a href="https://doi.org/10.5281/zenodo.15876646">https://doi.org/10.5281/zenodo.15876646</a></li> <li><strong>Figures and videos (media files):</strong> <a href="https://doi.org/10.5281/zenodo.7781916">https://doi.org/10.5281/zenodo.7781916</a></li> </ul> <p>The main repository is maintained at <a href="https://github.com/bruvellu/cephalic-furrow">https://github.com/bruvellu/cephalic-furrow</a>.</p>
Cdc42 couples T cell receptor endocytosis to GRAF1-mediated tubular invaginations of the plasma membrane
<p>This Dataset contains primary data used for the publication "Cdc42 couples T cell receptor endocytosis to GRAF1-mediated tubular invaginations of the plasma membrane" published online on 04. November 2019<br> doi:10.3390/cells8111388</p> <p><strong>Abstract:</strong> T cell activation is immediately followed by internalization of the T cell receptor (TCR).<br> TCR endocytosis is required for T cell activation, but the mechanisms supporting removal of TCR<br> from the cell surface remain incompletely understood. Here we report that TCR endocytosis is<br> linked to the clathrin-independent carrier (CLIC) and GPI-enriched endocytic compartments<br> (GEEC) endocytic pathway. We show that unlike the canonical clathrin cargo transferrin or the<br> adaptor protein Lat, internalized TCR accumulates in tubules shaped by the small GTPase Cdc42<br> and the Bin/amphiphysin/Rvs (BAR) domain containing protein GRAF1 in T cells. Preventing<br> GRAF1-positive tubules to mature into endocytic vesicles by expressing a constitutively active<br> Cdc42 impairs the endocytosis of TCR, while having no consequence on the uptake of transferrin.<br> Together, our data reveal a link between TCR internalization and the CLIC/GEEC endocytic route<br> supported by Cdc42 and GRAF1.</p> <p> </p> <p>Data are organised in compressed (.zip) folders entitled as the corresponding Figures in the publication.</p> <p>Programs we recommend to view the files are:<br> .fcs files: FlowJo software v10 (Tree Star, Ashland, OR, USA)<br> .lif files: LAS X v3 (Leica Microsystems, Wetzlar, Germany)<br> .pzfx files: Prism v7 software (GraphPad, San Diego, CA, USA)</p> <p> </p> <p>In case this Dataset is updated, new version will be available with doi:10.5281/zenodo.3545842</p>
Fig. 2. Invaginated protoscoleces isolated from a in Cystic echinococcosis in wild boars (Sus scrofa) from southern Italy: Epidemiological survey and molecular characterization
Fig. 2. Invaginated protoscoleces isolated from a fertile hydatid cyst.
Studying gastrulation by invagination: the bending of a cell sheet by mechanical cell properties using 3D deformable cell based simulations
<p>This dataset contains the scripts and end results of invagination simulation experiments.<br>The data are the results of a 3D cell based model that was used to investigate invagination: the bending of a cell sheet, and uses cell-cell adhesion, apical constriction, cell volume conservation, collision detection and handeling.</p>
Figure 9 in Five invaginations and shedding of the larval epidermis during development of the hoplonemertean Pantinonemertes californiensis (Nemertea: Hoplonemertea)
Figure 9. Fluorescein diacetate (FDA)-stained late rudiment stage larva of Pantinonemertes californiensis in the act of shedding cells of the larval epidermis. (A) Bright-field view; (B) a confocal projection of 21 1-µm sections of the same larva, showing the brightly- uorescent FDA-labelled cells of the transitory epidermis. Anterior is to the right. The larva was trapped on a slide, fixed by owing formaldehyde in seawater under the coverslip, and the image was collected immediately. Arrows highlight the same shedding cells in both images, which are brightly labelled with FDA.
Figure 8 in Five invaginations and shedding of the larval epidermis during development of the hoplonemertean Pantinonemertes californiensis (Nemertea: Hoplonemertea)
Figure 8. Roll-out epidermal map of phalloidin-labelled early invagination embryo (23.5-hour-old at 15–16◦C) of Pantinonemertes californiensis, showing cell outlines (a total of 80 large cells).
Figure 7 in Five invaginations and shedding of the larval epidermis during development of the hoplonemertean Pantinonemertes californiensis (Nemertea: Hoplonemertea)
Figure 7. Confocal projections of phalloidin-labelled larvae of Pantinonemertes californiensis showing surface cell outlines in the early invagination stage (A), early rudiment stage (B), late rudiment stage, which is contemporary with shedding of the larval epidermis (C), and the vermicular stage (D, E). At 15–16◦C these stages correspond to 23.5 hours (A), 2 days (B), 3 days (C) and 4 days (D, E) of development; ventral view, apical up. (E) An 11.5-µm sub-stack from the same stack as (D) shows the cell outlines without the interference of body wall muscles. (A) Mounted in Vectashield and scanned using 60 × Oil lens (NA 1.4); (B–E) mounted in phosphate-buffered saline and scanned using 60 × water lens (NA 1.2). Apical plate (ap), proboscis (pb), stomodeum (st), anterior invaginations (ai), remnants of posterior invaginations (pi∗), muscles (ms). Asterisks mark several provisional larval epidermis cells.
Figure 5 in Five invaginations and shedding of the larval epidermis during development of the hoplonemertean Pantinonemertes californiensis (Nemertea: Hoplonemertea)
Figure 5. Confocal micrographs of the late rudiment stage larvae of Pantinonemertes californiensis (3-day-old at 15–16◦C) labelled with phalloidin. This is the stage at which the larvae shed larval epidermal cells; apical is up. (A) A 10-µm sub-stack of frontal sections showing well-developed body wall muscles, the bipartite proboscis (pb) equipped with a muscle retractor (prm) and the dorsal commissure of the brain (dc); (B) a 5-µm sub-stack of frontal sections of a different larva showing the ventral commissure of the brain (vc), the lateral nerve cords (lnc) with the associated nerve cord muscles (nm), and proboscis insertion muscles (pim); (C) a 6.5-µm sub-stack of frontal sections of yet another larva showing the fused foregut (fgt) and midgut (mgt), and the proboscis pore (pp).
Figure 6 in Five invaginations and shedding of the larval epidermis during development of the hoplonemertean Pantinonemertes californiensis (Nemertea: Hoplonemertea)
Figure 6. Confocal micrographs of phalloidin-labelled vermicular stage larvae of Pantinonemertes californiensis; anterior is to the left. (A–C) Five-day-old larvae (12–13◦C). (A) An 8-µm sub-stack of frontal sections, showing cerebral ganglia (cg), lateral nerve cords (lnc) and nerve cord muscles (nm); (B) a 1-µm sagittal section, showing the proboscis (pb), foregut (fgt) and stomodeal opening (st). The position of the original proboscis pore (which is no longer apparent) is marked with an asterisk; (C) a 10-µm sub-stack of sagittal sections, illustrating the relative position of the dorsal commissure (dc) and lateral nerve cords with respect to proboscis; (D) confocal Z-projection (ventral view) of a 13-day-old larva, showing the well-developed circular, longitudinal and diagonal muscles of the body wall as well as the small cells that surround the stomodeum.
Figure 4 in Five invaginations and shedding of the larval epidermis during development of the hoplonemertean Pantinonemertes californiensis (Nemertea: Hoplonemertea)
Figure 4. Confocal micrographs of phalloidin-labelled early rudiment stage Pantinonemertes californiensis larvae. (A, C, D) Three-day-old larvae (12–13◦C); (B) 2-day-old larva (15–16◦C); apical pole up, ventral to the left in (A, C, D). (A) Lateral view, showing apical plate (ap) and the two shallow dimples at the anterior end – remnants of one of the anterior invaginations (ai1 and ai2); (B) a 15-µm frontal sub-stack showing the two forks of anterior invaginations (ai1 and ai2), the remnants of posterior invaginations (pi∗), posterior cirrus (pc) and midgut lumen (arrowhead); (C) a single sagittal 1-µm section showing the cerebral ganglia (cg) and lateral nerve cord (lnc); (D) same embryo as in (C), different 1-µm section showing the proboscis (pb), dorsal commissure (dc), and ventral commissure (vc) of the brain.
Figure 3 in Five invaginations and shedding of the larval epidermis during development of the hoplonemertean Pantinonemertes californiensis (Nemertea: Hoplonemertea)
Figure 3. Confocal micrographs of phalloidin-labelled early (A, B) and late (C, D) invagination stage larvae of Pantinonemertes californiensis. (A, B) A 28.5-hour-old prehatched embryo (12–13◦C); (C, D) a 46-hour-old (12–13◦C) larva; apical pole marked by the apical plate (ap) is up or upper right. (A) Confocal Z-projection (ventral view) showing stomodeum (st), proboscis rudiment (pb), paired anterior (ai) and posterior (pi) invaginations; (B) a 30-µm thick sub-stack of frontal sections showing the posterior cirrus (pc), paired anterior and posterior invaginations, proboscis and midgut lumen (arrowhead); (C) confocal Z-projection (ventral view), showing bifurcated anterior and posterior invaginations and the stomodeum (st); (D) a 29-µm thick sub-stack of frontal sections showing the five invaginations and midgut lumen (arrowhead).
Figure 1 in Five invaginations and shedding of the larval epidermis during development of the hoplonemertean Pantinonemertes californiensis (Nemertea: Hoplonemertea)
Figure 1. Cleavage in Pantinonemertes californiensis. (A) Fertilized egg in egg envelopes; (B) first polar body formation; (C) second polar body formation; (D) two-cell stage; (E) four-cell stage; (F) eight-cell stage; (G) 16-cell stage; (H) 32-cell stage. Scale bar 100 µm.
Figure 2 in Five invaginations and shedding of the larval epidermis during development of the hoplonemertean Pantinonemertes californiensis (Nemertea: Hoplonemertea)
Figure 2. Planuliform larva of Pantinonemertes californiensis. (A) Newly-hatched invagination stage larva of P. californiensis is uniformly ciliated, has an apical tuft (ap) and posterior cirrus (pc); (B) late rudiment stage larva (3 days old at 15–16◦C) has a distinct proboscis rudiment (pb) and two ocelli; (C) late rudiment stage larva in the process of shedding ciliated cells of its larval epidermis from around the mouth (m); (D) a chain of ciliated larval epidermal cells shed and left behind by a larva of P. californiensis. Scale bars 50 µm.
Duct-to-mucosa Versus Invagination for Pancreaticojejunostomy
ClinicalTrials.gov study NCT01695447. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Comparative Study Between Duct to Mucosa and Invagination Pancreaticojejunostomy After Pancreaticoduodenectomy:
ClinicalTrials.gov study NCT02142517. IPD Sharing: Not stated. Countries: 1. Publications: 7.
Comparison of Hernia Sac Ligation Versus Invagination
ClinicalTrials.gov study NCT05308251. IPD Sharing: UNDECIDED. Countries: 1. Publications: 6.
Studying the zippering process during gastrulation in Cnidaria: Aligning an invaginating germ layer with the help of filopodia using 3D deformable cell based simulations
<p>This dataset contains the scripts and end results of zippering simulation experiments.<br>The data are the results of a 3D cell based model that was used to investigate zippering aided invagination: Pulling the cell sheet inwards, and uses cell-cell adhesion, filopodia, apical constriction, cell volume conservation, collision detection and handeling. </p>
Text-fig. 4. Praoppiella oanae MIKO et MOUREK gen. et sp. nov. (holotype). A – dorsal view of the body (notogaster largely detached from body, rostral part of prodorsum partly invaginated); B – ventral view; C – dorsal view of detached part of notogaster; D – anterior margin of notogaster as drawed before detachment from the rest of the body; E – bothridium and sensillus. Bars indicating 50 µm (for A,B, C and D, above) and 25 µm (for E, below). For explanation of acronyms see page 31. in Oribatid Mite Fossils From Quaternary And Pre-Quaternary Sediments In Slovenian Caves I.Two New Genera And Two New Species Of The Family Oppiidae From The Early Pleistocene
Text-fig. 4. Praoppiella oanae MIKO et MOUREK gen. et sp. nov. (holotype). A – dorsal view of the body (notogaster largely detached from body, rostral part of prodorsum partly invaginated); B – ventral view; C – dorsal view of detached part of notogaster; D – anterior margin of notogaster as drawed before detachment from the rest of the body; E – bothridium and sensillus. Bars indicating 50 µm (for A,B, C and D, above) and 25 µm (for E, below). For explanation of acronyms see page 31.
Lateral Invagination of the Colorectal Anastomosis by Double Stapling
ClinicalTrials.gov study NCT04553250. IPD Sharing: NO. Countries: 0. Publications: 19.
ScienceDex guides
Understand access before you commit
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.