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111,247 results for “cells”
single-cell RNAseq data (data set 1) in the publication scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data
<p>The present dataset (dataset1) was used as input to build scFASTCORMICS models. The files correspond to the clusters identified by Seurat in the single-cell data from CRC samples downloaded from the GEO website (<strong>GSE81861). </strong></p> <p>see the protocol: scFASTCORMICS: A contextualization algorithm to reconstruct metabolic multi-cell population models from single-cell RNAseq data</p> <p>and github: https://github.com/sysbiolux/scFASTCORMICS</p> <p>For more information, version updates of the scFASTCORMICS. </p>
Force propagation between epithelial cell doublets
<p>Cell-generated forces play a major role in coordinating the large-scale behavior of cell assemblies, in particular during development, wound healing and cancer. Mechanical signals propagate faster than biochemical signals but can have similar effects, especially in epithelial tissues with strong cell-cell adhesion. However, a quantitative description of the transmission chain from force generation in a sender cell, force propagation across cell-cell boundaries, and the concomitant response of receiver cells is missing. For a quantitative analysis of this important situation, here we propose a minimal model system of two epithelial cells on an H-pattern ("cell doublet"). After optogenetically activating RhoA, a major regulator of cell contractility, in the sender cell, we measure the mechanical response of the receiver cell by traction force and monolayer stress microscopies. In general, we find that the receiver cells show an active response so that the cell doublet forms a coherent unit. However, force propagation and response of the receiver cell also strongly depend on the mechano-structural polarization in the cell assembly, which is controlled by cell-matrix adhesion to the adhesive micropattern. We find that the response of the receiver cell is stronger when the mechano-structural polarization axis is oriented perpendicular to the direction of force propagation, reminiscent of the Poisson effect in passive materials. We finally show that the same effects are at work in small tissues. Our work demonstrates that cellular organization and active mechanical response of a tissue is key to maintaining signal strength and leads to the emergence of elasticity, which means that signals are not dissipated like in a viscous system but can propagate over large distances. </p>
A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity
<p> </p> <p>In our manuscript, we utilized scRNA-seq libraries we generated from:</p> <p>-8 human psoriatic skin samples and 7 healthy control skin samples (ZIST.rds)</p> <p>-3 human psoriatic skin samples before and after tildrakizumab treatment (three_tildra_Trm1.rds) </p> <p>These *rds files are the Seurat objects for these data sets post-filtering and integration. For raw sequencing data corresponding to these samples, access can be found under accession number EGA: S00001005271.</p> <p>We also utilized bulk RNAseq data generated from CRISPR-Cas9 knockout of ZFP36L2 in human CD4 T cells from 3 different donors. The count matrices for each of these individual samples is uploaded here alongside a key explaining what each of the samples are with filenames that also correspond to the raw fastq files submitted at the European Genome-Phenome Archive (EGA), under accession number EGA: S00001005271. There are two replicates for each sample.</p> <p>All methods underlying the generation and analysis of these datasets can be found in the original manuscript: </p> <p>Cook CP, Taylor M, Liu Y, et al. A single-cell transcriptional gradient in human cutaneous memory T cells restricts Th17/Tc17 identity. <em>Cell Rep Med</em>. 2022;3(8):100715. doi:10.1016/j.xcrm.2022.100715</p> <p><br> Any additional questions or information requests can be addressed to Jeffrey.cheng@ucsf.edu or cook.675@berkeley.edu</p> <p> </p>
Dataset for Fast Li-ion Storage and Dynamics in TiO2 Nanoparticle Clusters Probed by Smart Scanning Electrochemical Cell Microscopy
<p>This dataset provides the raw data to the manuscript </p> <p><strong>"Fast Li-ion Storage and Dynamics in TiO<sub>2</sub> Nanoparticle Clusters Probed by Smart Scanning Electrochemical Cell Microscopy"</strong> published in Angewandte Chemie International Edition.</p> <p>Specifically, the following measurements are provided:</p> <ul> <li>Powder XRD data for the commercial anatase TiO<sub>2</sub>.</li> <li>Cyclic voltammetry data from SECCM measurements.</li> <li>SEM images of the TiO<sub>2</sub> nanoparticles after SECCM tip landing and electrochemical measurement.</li> </ul>
The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data
<p>In our work, we implemented the ABC-model and could show that one assay for measuring the openness of enhancers is sufficient. Further, we propose a generalised calculation of the ABC-score, which describes enhancer activity in a gene-specific manner, and which includes all TSS, without requiring any additional data. We combined our implementation of the ABC-score with an approach to quantify TF binding affinity into STARE: a framework to derive TF affinities to genes. STARE was also designed for potential application on single-cell data. You can find the code in our <a href="https://github.com/schulzlab/stare">GitHub repository</a> and more details in our <a href="https://doi.org/10.1093%2Fbioinformatics%2Fbtad062">publication</a>.</p> <p>We provide the data for the validation of our ABC-implementation on two CRISPR-screens. We also provide the results of our analysis of single-cell data of the human heart with STARE. All data is in hg19.</p> <p>Content:</p> <ul> <li>CRISPRi_screens: One file for each CRISPRi-screen with interactions that were used to plot precision-recall curves, containing columns for different ABC scoring versions.</li> <li>Enformer: Similar to the CRISPRi_screens, but containing columns for different calculations for Enformer's predicted expression change upon in silico mutagenesis of the enhancer region.</li> <li>K562_CandidateEnhancer: K562 enhancer with the 4th column for enhancer activity, one file for each activity representation that was measured.</li> <li>K562_ABC_Predictions: Regular ABC-scores and generalised ABC-scores for each activity measurement. The files contain all scored interactions for a 10MB window, without any cut-off. We also included the results of the implementation of the ABC-score of Fulco et al. (2019).</li> <li>STARE_Hocker_*: Whole STARE output for human heart single-cell data, one for regular ABC, generalised ABC, generalised ABC with average Hi-C matrix and one based on co-accessibility analysis. All approaches were run with a 5 MB window (except for GeneralisedABC500kb), the ABC-based runs with a score cut-off of 0.02. Each folder contains two subdirectories, one for the ABC-scoring and one for the Gene-TF affinity matrices. The 'ABC_output' also contains a GeneInfo file for each cell type, summarising different attributes per gene.</li> <li>INVOKE_Hocker_*: Folder with the input and output of INVOKE (see https://github.com/schulzlab/tepic), based on the STARE runs. CS genes stands for cell type-specific genes, defined as genes with a z-score across cell types of ≥ 2 and TPM ≥ 0.5. The INVOKE commands were as follows: <ul> <li>Rscript INVOKE.R --dataDir=<TF-Gene matrix> --outDir=<out_path> --response=Expression --regularization=E --performance=TRUE --outerCV=10 --seed=1234</li> </ul> </li> </ul> <p>Importantly, the results are based on data from the following publications:</p> <ul> <li>CRISPRi-screens: <ul> <li>Gasperini, Molly, Andrew J. Hill, José L. McFaline-Figueroa, Beth Martin, Seungsoo Kim, Melissa D. Zhang, Dana Jackson, et al. “A Genome-Wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.” <em>Cell</em> 176, no. 1–2 (January 2019): 377-390.e19. https://doi.org/10.1016/j.cell.2018.11.029.</li> <li> <p>Schraivogel, Daniel, Andreas R. Gschwind, Jennifer H. Milbank, Daniel R. Leonce, Petra Jakob, Lukas Mathur, Jan O. Korbel, Christoph A. Merten, Lars Velten, and Lars M. Steinmetz. “Targeted Perturb-Seq Enables Genome-Scale Genetic Screens in Single Cells.” <em>Nature Methods</em> 17, no. 6 (June 2020): 629–35. https://doi.org/10.1038/s41592-020-0837-5.</p> </li> <li> <p>Fulco, Charles P., Joseph Nasser, Thouis R. Jones, Glen Munson, Drew T. Bergman, Vidya Subramanian, Sharon R. Grossman, et al. “Activity-by-Contact Model of Enhancer–Promoter Regulation from Thousands of CRISPR Perturbations.” <em>Nature Genetics</em> 51, no. 12 (December 2019): 1664–69. https://doi.org/10.1038/s41588-019-0538-0.</p> </li> </ul> </li> <li>Enformer model: Avsec, Žiga, Vikram Agarwal, Daniel Visentin, Joseph R. Ledsam, Agnieszka Grabska-Barwinska, Kyle R. Taylor, Yannis Assael, John Jumper, Pushmeet Kohli, and David R. Kelley. “Effective Gene Expression Prediction from Sequence by Integrating Long-Range Interactions.” <em>Nature Methods</em> 18, no. 10 (October 2021): 1196–1203. https://doi.org/10.1038/s41592-021-01252-x.</li> <li>K562 predictions and average Hi-C matrix: Fulco, Charles P., Joseph Nasser, Thouis R. Jones, Glen Munson, Drew T. Bergman, Vidya Subramanian, Sharon R. Grossman, et al. “Activity-by-Contact Model of Enhancer–Promoter Regulation from Thousands of CRISPR Perturbations.” <em>Nature Genetics</em> 51, no. 12 (December 2019): 1664–69. https://doi.org/10.1038/s41588-019-0538-0.</li> <li>Hi-C matrix for K562 predictions: Rao, S. et al. (2014). A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell, 159(7), 1665–1680</li> <li>STARE and INVOKE runs: Hocker, J. D. et al. (2021). Cardiac cell type–specific gene regulatory programs and disease risk association. Science Advances, 7(20), eabf1444</li> <li>H3K27ac HiChIP for STARE runs: Anene-Nzelu, C. G. et al. (2020). Assigning Distal Genomic Enhancers to Cardiac Disease–Causing Genes. Circulation, 142(9), 910–912</li> <li>INVOKE software: Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction Schmidt et al., Nucleic Acids Research 2016; doi: 10.1093/nar/gkw1061</li> </ul> <p> </p>
Additional files of scTensor paper "scTensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data"
<p>Complex biological systems are described as a multitude of cell-cell interactions (CCIs). Recent single-cell RNA-sequencing studies focus on CCIs based on ligand-receptor (L-R) gene co-expression. However, the analytical methods are still not mature; such methods cannot detect CCIs and the related L-R pairs simultaneously or also are not appropriate to detect many-to-many CCIs.</p> <p>In this work, we propose scTensor, a novel method for extracting representative triadic relationships (or hypergraphs), which include ligand-expression, receptor-expression, and related L-R pairs. Through extensive studies with simulated and empirical datasets, we have shown that scTensor could detect some hypergraphs, which cannot be detected by conventional methods, especially when those CCIs are many-to-many relationships.</p>
Data for accurate cell type deconvolution in spatial transcriptomics using a batch effect-free strategy
<p>Simulated and experimental data used in the ReSort manuscript. It is necessary and sufficient to reproduce the results in the paper.</p>
Data set accompanying the paper "Effective cell membrane tension is independent of polyacrylamide substrate stiffness"
<p>This data set contains the data presented in the publication "Effective cell membrane tension is independent of polyacrylamide substrate stiffness". It consists of optical tweezers data and traction force microscopy data of 3T3 fibroblasts and Xenopus retinal ganglion cells on several different substrates.</p>
Correlation of the kinetics of viral antigen and genomic RNA with restoration of normal cell homeostasis
<p>The main objective of the studies within COCID Work Package 6 is to understand basic mechanisms by which viral replication machineries are removed from cells after pharmacological interruption of viral replication using functional as well as imaging techniques, including soft X-ray tomography.</p> <p>In this document, we highlight the progress in establishing the HCV replication models (replicons), the antiviral treatment chosen to eliminate viral structures from the host cells and the correlation between elimination of the viral replication machinery and restoration of a normal host cell homeostasis, using markers of HCV-induced stress. These data are essential to frame the experimental setup chosen for the imaging process required in subsequent stps of the project.</p>
Substrate stiffness reduces particle uptake by epithelial cells and macrophages in a size-dependent manner through mechanoregulation
<p>Cells continuously exert forces on their environment and respond to changes in mechanical forces by altering their behavior. Many pathologies such as cancer and fibrosis are hallmarked by dysregulation in the extracellular matrix, driving aberrant behavior through mechanotransduction pathways. We demonstrate that substrate stiffness can be used to regulate cellular endocytosis of particles in a size-dependent fashion. Culture of A549 epithelial cells and J774A.1 macrophages on polystyrene/glass (stiff) and polydimethylsiloxane (soft) substrates indicated that particle uptake is increased up to six times for A549 and two times for macrophages when cells are grown in softer environments. Furthermore, we altered surface characteristics through the attachment of submicron-sized particles as a method to locally engineer substrate stiffness and topography. To investigate the biomechanical changes which occurred within adherent epithelial cells, i.e. characterization of A549 cell spreading and focal adhesion maturation. Consequently, decreasing substrate rigidity and particle-based topography lead to a reduction of focal adhesion size. Moreover, expression levels of Yes-associated protein were found to correlate with the degree of particle endocytosis. A thorough appreciation of the mechanical cues may lead to improved solutions to optimize nanomedicine approaches for treatment of cancer and other diseases with abnormal mechanosignaling.</p>
Single-cell naïve IgM VH:VL sequence data from 22 Kymice
<p>Single-cell VH:VL sequencing data derived from naïve B-cells isolated from 22 Kymice. This dataset is published as part of the review process for the following preprint: https://www.biorxiv.org/content/10.1101/2022.06.27.497709v1. </p>
pSCoPE: Prioritized Single-Cell Proteomics (data for generating publication figures)
<p>Major aims of single-cell proteomics include increasing the consistency, sensitivity, and depth of protein quantification, especially for proteins and modifications of biological interest. To simultaneously advance all these aims, we developed prioritized Single Cell ProtEomics (pSCoPE). pSCoPE consistently analyzes thousands of prioritized peptides across all single cells (thus increasing data completeness) while analyzing identifiable peptides at full duty-cycle, thus increasing proteome depth. These strategies increased the sensitivity, data completeness, and proteome coverage over 2-fold. The gains enabled quantifying protein variation in untreated and lipopolysaccharide-treated primary macrophages. Within each condition, proteins covaried within functional sets, including phagosome maturation and proton transport. This protein covariation within a treatment condition was similar across the treatment conditions and coupled to phenotypic variability in endocytic activity. pSCoPE also enabled quantifying proteolytic products, suggesting a gradient of cathepsin activities within a treatment condition. pSCoPE is freely available and widely applicable, especially for analyzing proteins of interest without sacrificing proteome coverage. Support for pSCoPE is available at: <a href="http://scp.slavovlab.net/pSCoPE">scp.slavovlab.net/pSCoPE</a></p> <p> </p> <p>The files contained in this .zip directory are necessary for replicating the analysis and figures associated with the pSCoPE manuscript.</p> <p> </p>
Single-cell profiling identifies ACE+ granuloma macrophages as a non-permissive niche for intracellular bacteria during persistent Salmonella infection
<p>Macrophages mediate key antimicrobial responses against intracellular bacterial pathogens, such as <em>Salmonella enterica</em>. Yet, they can also act as a permissive niche for these pathogens to persist in infected tissues within granulomas, which are immunological structures comprised of macrophages and other immune cells. We apply single-cell transcriptomics to investigate macrophage functional diversity during persistent <em>Salmonella</em> <em>enterica</em> serovar Typhimurium (<em>S</em>Tm) infection in mice. We identify determinants of macrophage heterogeneity in infected spleens and describe populations of distinct phenotypes, functional programming, and spatial localization. Using a <em>S</em>Tm mutant with impaired ability to polarize macrophage phenotypes, we find that angiotensin converting enzyme (ACE) defines a granuloma macrophage population that is non-permissive for intracellular bacteria and their abundance anticorrelates with tissue bacterial burden. Disruption of pathogen control by neutralizing TNF is linked to preferential depletion of ACE<sup>+</sup> macrophages in infected tissues. Thus ACE<em><sup>+</sup></em> macrophages have limited capacity to serve as cellular niche for intracellular bacteria to establish persistent infection.</p>
Ultra-stable self-standing Au nanowires/TiO2 nanoporous membrane system for high-performance photoelectrochemical water splitting cells - Dataset
<p>Dataset of results presented in <em><strong>Mater. Horiz.</strong></em>, 2022,<strong>9</strong>, 2797-2808: Ultra-stable self-standing Au nanowires/TiO<sub>2</sub> nanoporous membrane system for high-performance photoelectrochemical water splitting cells.</p> <p>E. W. would like to acknowledge Alexander von Humboldt Foundation, Bonn, Germany, for funding the postdoctoral fellowship, and the Polish National Agency For Academic Exchange, Polish Returns Programme (Project no. BPN/PPO/ 2021/1/00002), and the National Science Centre, Poland (Project no. 2022/01/1/ST5/00019) for financial support of the project. G. S. would like to acknowledge the National Science Centre, Poland (Project no. 2016/23/B/ST5/00790). The authors thank C. Erdmann for performing the transmission electron microscopy measurements.</p>
Summary statistics of cell-type specific cis-eQTLs in eight brain cell-types
<p>This dataset contains eQTL summary statistics for all SNPs-gene pairs in 8 major brain cell types (within 1MB window surrounding the TSS of each expressed gene). For each cell type, there is one file per chromosome.</p> <p>Column description:</p> <p>1. Gene_id</p> <p>2. SNP_id</p> <p>3. Distance to TSS</p> <p>4. Nominal p-value</p> <p>5. Beta</p> <p>In addition, a file contains the SNP positions (snp_pos.txt) and tested allele.</p> <p>Update February 2023: The summary statistics from our 'tissue-like' analysis were added (pb[1-22].gz). These file contain eQTL summary statistics after aggregating all reads from all nuclei for each individual (instead of per cell type).</p>
Text-fig. 50. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c–f) images of "Foveolate seed sp. 2"; Catefica locality, Portugal. a, b) Lateral (a) and apical (b) views of seed showing the coarsely foveolate surface; note the truncate apex and the slightly depressed hilar-micropylar region; c) Longitudinal section (volume rendering cut between orthoslices xz0740 and xz0840) through the middle of seed showing the truncate apex with slightly depressed hilar-micropylar region and basal rounded chalazal region; note thick outer integument (oi) composed of an exotesta of thickwalled palisade-like cells and a thin inner integument (ii); d, e, f) Transverse (d, orthoslice xy0800) and longitudinal sections (e, orthoslice xz1100, f, orthoslice yz0800) through seed hilar-micropylar region, showing the exotesta comprised of the thick-walled palisade-like cells of the outer integument (oi), small, thin-walled meso- endotestal cells of the outer integument (arrows) and thin inner integument (ii). Specimen, Catefica 153-S172332 (a–f). Scale bars = 300 Μm (a–f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 50. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c–f) images of "Foveolate seed sp. 2"; Catefica locality, Portugal. a, b) Lateral (a) and apical (b) views of seed showing the coarsely foveolate surface; note the truncate apex and the slightly depressed hilar-micropylar region; c) Longitudinal section (volume rendering cut between orthoslices xz0740 and xz0840) through the middle of seed showing the truncate apex with slightly depressed hilar-micropylar region and basal rounded chalazal region; note thick outer integument (oi) composed of an exotesta of thickwalled palisade-like cells and a thin inner integument (ii); d, e, f) Transverse (d, orthoslice xy0800) and longitudinal sections (e, orthoslice xz1100, f, orthoslice yz0800) through seed hilar-micropylar region, showing the exotesta comprised of the thick-walled palisade-like cells of the outer integument (oi), small, thin-walled meso- endotestal cells of the outer integument (arrows) and thin inner integument (ii). Specimen, Catefica 153-S172332 (a–f). Scale bars = 300 Μm (a–f).
Text-fig. 49. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c–e) images of "Foveolate seed sp. 1"; Catefica locality, Portugal. a) Lateral view of seed showing foveolate surface; note the slightly pointed hilar-micropylar region with the preservation of a presumed secretion (arrow) from the micropyle; b) Detail of seed surface showing shallow pitting and very faint outlines of the undulate anticlinal walls of the exotestal cells; c) Longitudinal section (volume rendering cut between orthoslices yz0450 and yz0460) through the middle of the seed showing the slightly pointed hilarmicropylar region and the rounded chalazal region; note the thick exotesta of the outer integument composed of thick-walled palisade-like cells (oi); note partial preservation of large cells of the nutritive tissue (nu) and the smaller cells of the embryo (em) at the micropylar end of the seed; d, e) Longitudinal sections (d, orthoslice xz0750, e, orthoslice yz0485) through middle of the seed perpendicular to each other showing the hilar-micropylar region with the preservation of a presumed secretion from micropyle (e, arrow), thick palisade-like cells of outer integument (oi), larger cells of the nutritive tissue (nu) and remains of the smaller cells of the embryo (em). Specimen, Catefica 49-S172316 (a–e). Scale bars = 300 Μm (a, c–e), 50 Μm (b). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 49. Scanning electron microscope (SEM, a, b) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c–e) images of "Foveolate seed sp. 1"; Catefica locality, Portugal. a) Lateral view of seed showing foveolate surface; note the slightly pointed hilar-micropylar region with the preservation of a presumed secretion (arrow) from the micropyle; b) Detail of seed surface showing shallow pitting and very faint outlines of the undulate anticlinal walls of the exotestal cells; c) Longitudinal section (volume rendering cut between orthoslices yz0450 and yz0460) through the middle of the seed showing the slightly pointed hilarmicropylar region and the rounded chalazal region; note the thick exotesta of the outer integument composed of thick-walled palisade-like cells (oi); note partial preservation of large cells of the nutritive tissue (nu) and the smaller cells of the embryo (em) at the micropylar end of the seed; d, e) Longitudinal sections (d, orthoslice xz0750, e, orthoslice yz0485) through middle of the seed perpendicular to each other showing the hilar-micropylar region with the preservation of a presumed secretion from micropyle (e, arrow), thick palisade-like cells of outer integument (oi), larger cells of the nutritive tissue (nu) and remains of the smaller cells of the embryo (em). Specimen, Catefica 49-S172316 (a–e). Scale bars = 300 Μm (a, c–e), 50 Μm (b).
Text-fig. 48. Scanning electron microscope (SEM, a, b, d–i) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c) images of "One-seeded fruit sp. 2" (a–c), "Unassigned, unnamed fruits" (d–f), Pazliopsis sp. (g, h) and "Follicular fruit with exotestal seeds" (i); Catefica locality, Portugal. a) Lateral view of fruit showing remains of tepals (te) and a single stamen (st); b) Detail of fruit surface showing short, scale-like, peltate trichomes (arrows); c) Transverse section (orthoslice xy0475) of fruit containing a single seed showing tepals (te) and fruit surface with peltate trichomes (arrow); note partial preservation of internal nutritive tissue; d) Fruit in lateral view showing the almost smooth epidermis with scattered openings; e) Detail of fruit surface from (d) showing the scattered openings in the epidermis interpreted as burst secretory cells (arrows); f) Dorsi-ventral view of tiny fruit with an irregular surface; g) Lateral view of exotestal seed assigned to cf. Pazliopsis sp.; h) Detail of fruit surface of seed in (g) showing faint facets of outer palisade layer with fine jigsaw-puzzle outlines of the anticlinal walls; i) Lateral view of fragmentary follicular fruit showing two exposed exotestal seeds. Specimens, Catefica 153-S174314 (a–c), Catefica 50-S170420 (d, e), Catefica 152-S174300 (f), Catefica 49-S172319 (g, h), Catefica MM158-P0272 (i). Scale bars = 300 Μm (a, c, d, f, g, i), 100 Μm (e), 50 Μm (b, h). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 48. Scanning electron microscope (SEM, a, b, d–i) and synchrotron radiation X-ray tomographic microscopy (SRXTM, c) images of "One-seeded fruit sp. 2" (a–c), "Unassigned, unnamed fruits" (d–f), Pazliopsis sp. (g, h) and "Follicular fruit with exotestal seeds" (i); Catefica locality, Portugal. a) Lateral view of fruit showing remains of tepals (te) and a single stamen (st); b) Detail of fruit surface showing short, scale-like, peltate trichomes (arrows); c) Transverse section (orthoslice xy0475) of fruit containing a single seed showing tepals (te) and fruit surface with peltate trichomes (arrow); note partial preservation of internal nutritive tissue; d) Fruit in lateral view showing the almost smooth epidermis with scattered openings; e) Detail of fruit surface from (d) showing the scattered openings in the epidermis interpreted as burst secretory cells (arrows); f) Dorsi-ventral view of tiny fruit with an irregular surface; g) Lateral view of exotestal seed assigned to cf. Pazliopsis sp.; h) Detail of fruit surface of seed in (g) showing faint facets of outer palisade layer with fine jigsaw-puzzle outlines of the anticlinal walls; i) Lateral view of fragmentary follicular fruit showing two exposed exotestal seeds. Specimens, Catefica 153-S174314 (a–c), Catefica 50-S170420 (d, e), Catefica 152-S174300 (f), Catefica 49-S172319 (g, h), Catefica MM158-P0272 (i). Scale bars = 300 Μm (a, c, d, f, g, i), 100 Μm (e), 50 Μm (b, h).
Text-fig. 47. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of "One-seeded fruit sp. 1"; Catefica locality, Portugal. a, b) Lateral view of fruits showing slightly sinuous ventral margin and the curved stalk; c, d) Longitudinal sections perpendicular to each other through the median part of fruit and its single seed (c, orthoslice yz0652, d, xz0739) showing the bitegmic seed closely adhering to the fruit wall (fw); the several cell layer thick outer integument (oi) and the membranous inner integument (ii); note the vascular bundle (vb) branching into a dorsal and lateral bundle near the base of the fruit; e) Transverse section (orthoslice xy0600) showing fruit wall (fw) and outer (oi) and inner (ii) integuments of the seed; f) Longitudinal section (orthoslice yz0871) through the micropylar region showing micropyle (mi) formed from membranous inner integument (ii). Specimens, Catefica 49-S174927 (a), Catefica 49-S174923 (b, f), Catefica 49-S174769 (c–e). Scale bars = 300 Μm (a–d), 100 Μm (e, f). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 47. Synchrotron radiation X-ray tomographic microscopy (SRXTM) images of "One-seeded fruit sp. 1"; Catefica locality, Portugal. a, b) Lateral view of fruits showing slightly sinuous ventral margin and the curved stalk; c, d) Longitudinal sections perpendicular to each other through the median part of fruit and its single seed (c, orthoslice yz0652, d, xz0739) showing the bitegmic seed closely adhering to the fruit wall (fw); the several cell layer thick outer integument (oi) and the membranous inner integument (ii); note the vascular bundle (vb) branching into a dorsal and lateral bundle near the base of the fruit; e) Transverse section (orthoslice xy0600) showing fruit wall (fw) and outer (oi) and inner (ii) integuments of the seed; f) Longitudinal section (orthoslice yz0871) through the micropylar region showing micropyle (mi) formed from membranous inner integument (ii). Specimens, Catefica 49-S174927 (a), Catefica 49-S174923 (b, f), Catefica 49-S174769 (c–e). Scale bars = 300 Μm (a–d), 100 Μm (e, f).
Text-fig. 46. Scanning electron microscope (SEM) images of "Rugulate fruit"; Catefica locality, Portugal. a, b) Lateral (a) and ventral (b) views of a rugulate fruit showing the short extension of the sessile stigma at the apex (arrows); c) Irregular surface of fruit that probably reflects an irregular endocarp; note the isodiametric outlines of the epidermal cells; d) Semi-tectate reticulate pollen grains embedded in the remains of a secretion on the stigmatic surface. Specimen, Catefica 154-S101291 (a–d). Scale bars = 300 Μm (a, b), 100 Μm (c), 6 Μm (d). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 46. Scanning electron microscope (SEM) images of "Rugulate fruit"; Catefica locality, Portugal. a, b) Lateral (a) and ventral (b) views of a rugulate fruit showing the short extension of the sessile stigma at the apex (arrows); c) Irregular surface of fruit that probably reflects an irregular endocarp; note the isodiametric outlines of the epidermal cells; d) Semi-tectate reticulate pollen grains embedded in the remains of a secretion on the stigmatic surface. Specimen, Catefica 154-S101291 (a–d). Scale bars = 300 Μm (a, b), 100 Μm (c), 6 Μm (d).
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.