284 Works

Activation of alpha-globin transcription in primary mouse erythroid progenitors

Robert Beagrie & A. Marieke Oudelaar
Mammalian gene expression patterns are controlled by regulatory elements, which interact within Topologically Associating Domains (TADs). The relationship between activation of regulatory elements, formation of structural chromatin interactions and gene expression during development is unclear. Here, we present Tiled-C, a low-input Chromosome Conformation Capture (3C) technique. We use this approach to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. In this dataset, we measure nascent transcription of the...

High-content image-based drug screen identifies a clinical compound against cell transmission of adenovirus

Fanny Georgi
Screen Description Human adenovirus infected quality control plates consisting solely on the solvent control DMSO to confirm assay stability prior to Z' plates (preZ) and screen (preScreen).

An Image-Based Data-Driven Analysis of Cellular Architecture in a Developing Tissue

Jonas Hartmann
A data-driven analysis of cell morphology and intracellular organization in the developing zebrafish posterior lateral line primordium, a model tissue for the study of self-organized morphogenesis. 3D image stacks were acquired using AiryScan FAST-mode confocal fluorescence microscopy. Automated single-cell segmentation and point cloud-based morphometry were developed to extract numerical features representing cell morphology and intracellular protein distributions. Machine learning was used with the extracted numerical features to perform data integration across experiments and context-guided data...

Timing of gene expression in a cell-fate decision system

Aymoz , Solé , Pierre , Schmitt, de Nadal, Posas & Pelet
During development, morphogens provide extracellular cues allowing cells to select a specific fate by inducing complex transcriptional programs. The mating pathway in budding yeast offers simplified settings to understand this process. Pheromone secreted by the mating partner triggers the activity of a MAPK pathway, which results in the expression of hundreds of genes. Using a dynamic expression reporter, we quantified the kinetics of gene expression in single cells upon exogenous pheromone stimulation and in the...

Ex vivo live cell tracking in kidney organoids using light sheet fluorescence microscopy

Marie Held
All assays were performed on live cultures. The intact kidney rudiments were cultured at air liquid interface for 4 days following dissection. The organoids were cultured under medium immersion for six days following dissection. The samples cultured at air liquid interface were gently removed from the membranes before starting the assay. The samples were incubated for one hour at 25ºC with PBS containing 1uM 5(6)-Carboxyfluorescein (6-CF) and 20 ug/ml of PNA (Vector Laboratories). For the...

Multi-fluorescence high-resolution episcopic microscopy (MF-HREM) for three dimensional imaging of adult murine organs

Claire Walsh
Multi-fluorescent High Resolution Episcopic Microscopy (MF-HREM) is a serial-sectioning, block-facing, wide-field fluorescence technique. It can image large volumes (>0.5mm3) at high resolution (~2um) without the need for tissue clearing or optical sectioning. We detail developments in sample processing including stain penetration, resin embedding and imaging. In addition, we describe image post-processing methods needed to segment and further quantify these data. Finally, we demonstrate the wide applicability of MF-HREM by: 1) quantifying adult mouse glomeruli. 2)...

Ex vivo live cell tracking in kidney organoids using light sheet fluorescence microscopy

Marie Held
We have adapted the mouse kidney rudiment assay to generate renal organoids. To demonstrate that the organoid culture method of re-aggregated kidney rudiments in PDMS discs resulted in 3D kidney organoids with organotypic structures, we stained fixed six day old organoids for various developmental markers and imaged them with a light sheet fluorescent microscope. We have stained for the following markers: Megalin, Laminin, Cytokeratin, Pax2, Six2, Wt1, Synaptopodin and Nephrin and have also used the...

Ex vivo live cell tracking in kidney organoids using light sheet fluorescence microscopy

Marie Held
We have adapted the mouse kidney rudiment assay to generate renal organoids. We have immunostained endpoint fixed organoids and E13.5 embryonic kidneys and imaged them with a light sheet fluorescent microscope. The data generated for this manuscript is made accessible here and includes immunofluorescence staining after end point fixation revealing that organotypic structures develop within the organoids. Furthermore, we have performed an assay to ascertain tubular functionality. Following, we have imaged organoids containing Wt1-GFP knock-in...

Confocal microscopy images

Wang
Confocal microscopy images: All of the samples after shear stress treatment were observed using Leica confocal microscopy. The images show fields of view under microscopy. Excel chart for data analysis: Bacterial counting was performed by the software Image J, and analysed using Excel.

OCT-MoS, a dataset of mouse skin squamous cell carcinoma stages by full-field optical coherence tomography

Manuel Calderón Delgado
The incidence of cutaneous squamous cell carcinoma (SCC) has increased in recent years, while it remains as an understudied subject. Current methods for the diagnose of skin cancer are either invasive, present a low resolution, or images that are difficult to interpret. Full-field optical coherence tomography (FF-OCT) has proven its potential as a non-invasive imaging technique of epithelial tissue. The sub-micrometer resolution offered by FF-OCT is able to show fine features such as cell nuclei,...

A machine learning approach to define antimalarial drug action from heterogeneous cell-based screens

Jake Baum
Drug resistance threatens the effective prevention and treatment of an ever-increasing range of human infections. This highlights an urgent need for new and improved drugs with novel mechanisms of action to avoid cross-resistance. Current cell-based drug screens are, however, restricted to binary live/dead readouts with no provision for mechanism of action prediction. Machine learning methods are increasingly being used to improve information extraction from imaging data. Such methods, however, work poorly with heterogeneous cellular phenotypes...

A Reference Library for Characterizing Protein Subcellular Localizations by Image-Based Machine Learning

David Andrews
Libraries composed of 789,011 and 523,319 optically validated reference confocal micrographs of 17 and 20 EGFP fusion proteins localized at key cell organelles as landmarks in murine and human cells were generated for assignment of subcellular localization in mammalian cells. For each image of individual cells, 160 morphology and statistical features were used to train a random forests classifier to automatically assign the localization of proteins and dyes in both cell types and to analyze...

A Reference Library for Characterizing Protein Subcellular Localizations by Image-Based Machine Learning

David Andrews
Libraries composed of 789,011 and 523,319 optically validated reference confocal micrographs of 17 and 20 EGFP fusion proteins localized at key cell organelles as landmarks in murine and human cells were generated for assignment of subcellular localization in mammalian cells. For each image of individual cells, 160 morphology and statistical features were used to train a random forests classifier to automatically assign the localization of proteins and dyes in both cell types and to analyze...

A Reference Library for Characterizing Protein Subcellular Localizations by Image-Based Machine Learning

David Andrews
Libraries composed of 789,011 and 523,319 optically validated reference confocal micrographs of 17 and 20 EGFP fusion proteins localized at key cell organelles as landmarks in murine and human cells were generated for assignment of subcellular localization in mammalian cells. For each image of individual cells, 160 morphology and statistical features were used to train a random forests classifier to automatically assign the localization of proteins and dyes in both cell types and to analyze...

A quantitative map of human Condensins provides new insights into mitotic chromosome architecture

Jan Ellenberg
FRAP experiments of Condensin-mEGFP subunits on the metaphase plate.

A quantitative map of human Condensins provides new insights into mitotic chromosome architecture

Jan Ellenberg
Single Colour - Condensin subunits were immunostained (with an anti-GFP antibody), and mitotic cells with chromatids oriented in parallel to the focal plane were selected for imaging. DNA (Hoechst) and Condensins (mEGFP tag and anti-GFP immunostaining) were imaged by diffraction-limited microscopy, whereas immunostained Condensin was also imaged by STED microscopy. Double Colour - NCAPH2-mEGFP and NCAPH-Halo were immunostained respectively with anti-GFP (1:500; ab13970; Abcam) + goat secondary anti-chicken Alexa Fluor 594 (1;500; A-11042; Thermo Fisher...

Distinct Roles of Tumor Associated Mutations in Collective Cell Migration

Rachel Lee & Stuart Martin
Recent evidence suggests that groups of cells are more likely to form clinically dangerous metastatic tumors, emphasizing the importance of understanding mechanisms underlying collective behavior. The emergent collective behavior of migrating cell sheets in vitro has been shown to be disrupted in tumorigenic cells but the connection between this behavior and in vivo tumorigenicity remains unclear. We use particle image velocimetry to measure a multidimensional migration phenotype for genetically defined human breast epithelial cell lines...

Image Data from Transfer and Persistence of UV powder trace material

Christian Cole, Melissa Lawson, Stephanie Green, Stewart Doyle, Emma Macneill & Bethany Hamilton
Dataset of 2718 raw images taken for the study of transfer and persistence of UV powder deposited on a variety of clothing material. This dataset constitutes a ground truth for use as a model for forensic trace evidence.

In Toto Cell Tracking using Lightsheet Microscopy of the Neuromesodermal Progenitor Zone of the Zebrafish Tailbud from the 21st Somite Stage

Benjamin Steventon
Lightsheet microscopy has been previously used to image and directly study the process of gastrulation in a zebrafish embryo. Before now it was not possible to use this method to study late-stage somatogenesis, due to the movement of the embryo, resulting in displacement from the field of view. Here we achieve 4D lightsheet imaging with online, image based registration to maintain the field of view during long timelapses, with emphasis on the tailbud. The zebrafish...

Distinct Roles of Tumor Associated Mutations in Collective Cell Migration

Rachel Lee & Stuart Martin
Recent evidence suggests that groups of cells are more likely to form clinically dangerous metastatic tumors, emphasizing the importance of understanding mechanisms underlying collective behavior. The emergent collective behavior of migrating cell sheets in vitro has been shown to be disrupted in tumorigenic cells but the connection between this behavior and in vivo tumorigenicity remains unclear. We use particle image velocimetry to measure a multidimensional migration phenotype for genetically defined human breast epithelial cell lines...

3D super-resolution fluorescence microscopy maps the variable molecular architecture of the Nuclear Pore Complex

Jan Ellenberg
We explored the power of 3D super-resolution microscopy combined with computational classification and averaging to explore the 3D structure of the NPC in single human cells. We show that this approach can build the first integrated 3D structural map containing both central as well as peripheral NPC subunits with molecular specificity and nanoscale resolution. Our unbiased classification of over ten thousand individual NPCs indicates that the nuclear ring and the nuclear basket can adopt different...

Live imaging screen reveals that TYRO3 and GAK ensure accurate spindle positioning in human cells

Benita Wolf, Coralie Busso & Pierre Gönczy
Proper spindle positioning is crucial for spatial cell division control. Spindle positioning in human cells relies on a ternary complex comprising Gαi1-3, LGN and NuMA, which anchors dynein at the cell cortex, thus enabling pulling forces to be exerted on astral microtubules. We developed a live imaging siRNA-based screen using stereotyped fibronectin micropatterns to uncover components modulating spindle positioning in human cells, testing 1280 genes, including all kinases and phosphatases. We thus discover 16 components...

Hydrocarbon pollutant impact on spectral and biophysical properties of willow and grass species

Raquel Serrano-Calvo
Vegetation is a potential indicator of land contaminated by hydrocarbons. Remote sensing holds great potential for detecting stress in vegetation caused by the presence of hydrocarbons, but as yet this potential has not been realised, largely due to a lack of understanding of the biophysiological impacts of hydrocarbons on plant growth, and the specific spectral expression of them. Previous research has demonstrated success in laboratory simulation of hydrocarbon contamination and the analysis of the spectral...

HDBR Atlas: Gene Expression in Early Human Development

Janet Kerwin, YuZhu Cheng, Steven Lisgo, Andrew Copp & Deborah Henderson
Gene expression studies in early human development from 3 to 19 post conceptional weeks (PCW).

Multi-scale imaging and analysis identifies pan-embryo cell dynamics of germlayer formation in zebrafish

Gopi Shah, Nico Scherf & Jan Huisken
The coordination of cell movements across spatio-temporal scales ensures precise positioning of organs during vertebrate gastrulation. Mechanisms governing such morphogenetic movements have been studied only within a local region, a single germlayer or in whole embryos without cell identity. Scale-bridging imaging and automated analysis of cell dynamics are needed for a deeper understanding of tissue formation during gastrulation. Here we report pan-embryo analyses of formation and dynamics of all three germlayers simultaneously within a developing...

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