45 Works

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...

In situ genome sequencing resolves DNA sequence and structure in intact biological samples

Edward S. Boyden, Jason Buenrostro & Fei Chen
Understanding genome organization requires integration of DNA sequence and 3D spatial context, however, existing genome-wide methods lack either base-pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across...

In situ genome sequencing resolves DNA sequence and structure in intact biological samples

Edward S. Boyden, Jason Buenrostro & Fei Chen
Understanding genome organization requires integration of DNA sequence and 3D spatial context, however, existing genome-wide methods lack either base-pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across...

Quantification of Bone Marrow Compartments in Histological Sections

Josefine Tratwal & Olaia Naveiras
MarrowQuant, a digital and quantitative pathology tool was used to quantify the different compartments within the bone marrow at different conditions, mainly aplasia and aging conditions. By using our tool, we can compare the skeletal map induced by lethal irradiation(aplasia), with longitudinal quantification of the “red-to-yellow-to-red” transition over 2 months (aging) in C57BL/6 mouse femurs and tibiae.

Supporting data for “A Systematic Study of the In Vitro Pharmacokinetics and Estimated Human In Vivo Clearance of Indole and Indazole-3-Carboxamide Synthetic Cannabinoid Receptor Agonists Detected on the Illicit Drug Market”

Andrew Brandon, Craig McKenzie, Lysbeth Antonides & Kevin Read
This dataset comprises supporting information for the peer-reviewed manuscript: A Systematic Study of the In Vitro Pharmacokinetics and Estimated Human In Vivo Clearance of Indole and Indazole-3-Carboxamide Synthetic Cannabinoid Receptor Agonists Detected on the Illicit Drug Market published in the journal ‘Molecules’.

High content genome-wide siRNA screen to investigate the coordination of cell size and RNA production

Micha Müller
Coordination of RNA abundance and transcription rates with cell size has been observed in diverse organisms and isogenic cell populations. However, how cells achieve such ‘size-scaling’ of transcription is unknown. Here we describe a genome-wide siRNA screen to find novel regulators of global RNA production in human cells. We quantify single-cell RNA production rates using metabolic pulse-labelling of RNA and subsequent high-content imaging. Our quantitative, single-cell measurements of DNA, nascent RNA, proliferating cell nuclear antigen...

Adverse positioning in mammography - observations of imaging features

Patsy Whelehan
This dataset consists of observations of mammographic images, plus three relevant variables used in the validation process for the measure of adverse positioning we developed based on the dataset. An expert observer generated the primary data by reviewing mammographic images to judge the presence or absence of a set of features developed through theory and consultation with other experts. The data can be reused by anyone wishing to learn and practice psychometric validation techniques, for...

High performance SERS platforms via parametric optimization of laser-assisted photodeposition of silver and gold nanoparticles

Manuel Hoffmann, Stefan Wackerow, Amin Abdolvand & Svetlana Zolotovskaya
Parametric optimization of laser-assisted photocatalytic growth of Ag and Au nanoparticles for high SERS enhancement factor performance informed by design of experiment is demonstrated. The photodeposition process was divided into two phases – seeding and growth – in order to achieve the highest possible nanoparticle surface coverage for the size range from 10 to 100 nm. Substantial difference in the parameter effects between the Ag and Au seeding and growth was found. SERS performance of...

Multiscale modelling of cancer evolution: the role of fibres and macrophages in invasion patterns

Szabolcs Süveges
The ability to invade its surrounding tissue is one of the acknowledged hallmarks of cancer. This complex multi-scale process is affected by many players of the tumour microenvironment (TME), including the extracellular matrix (ECM) and various stromal cells such as macrophages. One of these key processes is the secretion of matrix degrading enzymes that enables the degradation of the neighbouring ECM and cell-matrix adhesion. By varying the strength of cell-matrix and multiple cell-cell adhesions, cancer...

Centrifuge dataset for screw pile installation and uplift

Benjamin Cerfontaine
The dataset describes the installation and uplift loading of a screw piles in a sand bed prepared by dry pluviation. The full details of the procedure can be found in the related paper. The different phases of each test are described in Figure 1. The data sampling rate is equal to 10ms. 1. The centrifuge is spun up to the final g-level (50g at mid-depth of the pile). 2. A period of rest (few minutes)....

QMB Morning Dataset

Tamas Suveges
The proliferation of wearable cameras has accelerated and facilitated a surge in research on analysis of egocentric videos. This relatively new field has relatively few research datasets. A significant share of publicly available egocentric datasets is purposely acquired for activity recognition, video summarization, object detection, and behavioural understanding. Here we share our dataset that is focused on personal localization and mapping. We collected our dataset on the university campus, documenting a user’s typical morning. The...

Homologous chromosomes undergo sequential quasi-stable interactions during meiotic prophase

Assaf Zaritsky
Deep learning has emerged as the technique of choice for identifying hidden patterns in cell imaging data, but is often criticized as ‘black-box’. Here, we demonstrate that a generative neural network captures subtle details of cell appearance, which permit the prediction of the metastatic efficiency of patient-derived melanoma xenografts with known clinical outcomes. To probe the predictor, we used the network to generate “in-silico” cell images that amplified the critical predictive cellular features. These images...

Homologous chromosomes undergo sequential quasi-stable interactions during meiotic prophase

Trent Newman
The pairing of homologous chromosomes in meiosis I is essential for sexual reproduction and is mediated, in part, by the formation and repair of Spo11-induced DNA double strand breaks (DSBs). In budding yeast, each cell receives 150-200 DSBs, yet only a fraction go on to form crossover products. How and why the cell initially coordinates so many interactions along each chromosome is not well understood. Using a fluorescent reporter-operator system (FROS), we measure the kinetics...

Whole-organ analysis of TGF-beta-mediated remodelling of the tumour microenvironment by tissue clearing

Shimpei I. Kubota
Tissue clearing is one of the most powerful strategies for a comprehensive analysis of disease progression. Here, we established an integrated pipeline that combines tissue clearing, 3D imaging, and machine learning and applied to a mouse tumour model of experimental lung metastasis using human lung adenocarcinoma A549 cells. This pipeline provided the spatial information of the tumour microenvironment. We further explored the role of transforming growth factor-beta (TGF-beta) in cancer metastasis. TGF-beta-stimulated cancer cells enhanced...

Cell health phenotypes can be predicted from unbiased image-based morphology readouts

Gregory Way
Genetic and chemical perturbations impact diverse cellular phenotypes, including multiple indicators of cell health. These readouts reveal toxicity and antitumorigenic effects relevant to drug discovery and personalized medicine. We present an approach to predict multiple cell health phenotypes using Cell Painting, an inexpensive and scalable image-based morphology assay. In matched CRISPR perturbations of three cancer cell lines, we collected both Cell Painting data and targeted assay readouts from seven reagents that measure specific cell health...

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,...

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,...

HIV-1 fusion is disrupted by addition of deoxygluose and is rescued with addition of cholesterol

Sergi Padilla-Parra
There has been resurgence in determining the role of host metabolism in viral infection yet deciphering how the metabolic state of single cells affects viral entry and fusion remains unknown. Here, we have developed a novel assay multiplexing genetically-encoded biosensors with single virus tracking (SVT) to evaluate the influence of global metabolic processes on the success rate of virus entry in single cells. We found that cells with a lower ATP:ADP ratio prior to virus...

Nunalleq Educational Resource Archived Media Content

Alice Watterson
Media content to archive for the Nunalleq Educational Resource project (2017-2019). This contains an organised folder structure containing 3D model files, audio files, video files as well as text and photoshop files outlining the structure of the original resource. Additionally we have provided a 'walkthrough' video which demonstrated how the interactions work within the resource. The installers for the current resource build which were distributed to schools in Alaska and made available for public download...

Quantification of Bone Marrow Compartments in Histological Sections

Josefine Tratwal & Olaia Naveiras
We report the development of a semi-automated image analysis plug-in, MarrowQuant, which employs the open-source software QuPath, to systematically quantify multiple bone components in H&E sections in an unbiased manner. MarrowQuant discerns and quantifies the areas occupied by bone, adipocyte ghosts, hematopoietic cells and the interstitial/microvascular compartment. A separate feature, AdipoQuant, fragments adipocyte ghosts in H&E-stained sections of extramedullary adipose tissue sections to render adipocyte area and size distribution. Quantification of BM hematopoietic cellularity with...

Dynamics of Drosophila endoderm specification

Shannon Keenan
During early Drosophila embryogenesis, a network of gene regulatory interactions orchestrates terminal patterning, playing a critical role in the subsequent formation of the gut. We utilized CRISPR gene editing at endogenous loci to create live reporters of transcription and light-sheet microscopy to monitor the individual components of posterior patterning network across 90 minutes prior to gastrulation. We developed a computational pipeline for fusing imaging datasets of the individual components into a common multivariable trajectory. This...

Image-based deep learning reveals the responses of human motor neurons to stress and VCP-related ALS

Rickie Patani & Raphaelle Luisier
The aim of the study was to investigate relationships between ALS-related RNA-binding proteins and ALS, under different stress conditions.

Diffusion-mediated HEI10 coarsening can explain meiotic crossover positioning in Arabidopsis

Christopher Morgan
In most organisms, the number and distribution of crossovers that occur during meiosis are tightly controlled. All chromosomes must receive at least one “obligatory crossover” and crossovers are prevented from occurring near one another by “crossover interference”. However, the mechanistic basis of this phenomenon of crossover interference has remained mostly mysterious. Using quantitative super-resolution cytogenetics and mathematical modelling, we investigated crossover positioning in the Arabidopsis thaliana wild-type, an over-expressor of the conserved E3 ligase HEI10,...

Live imaging of remyelination in the adult mouse corpus callosum

Sebastian Jessberger & Sara Bottes
Oligodendrocyte precursor cells (OPCs) retain the capacity to remyelinate axons in the corpus callosum (CC) upon demyelination. However, the dynamics of OPC activation, mode of cell division, migration, and differentiation on a single cell level remain poorly understood due to the lack of longitudinal observations of individual cells within the injured brain. After inducing focal demyelination with lysophosphatidylcholin (LPC) in the CC of adult mice, we used 2-photon microscopy to follow for up to 2...

Root reinforcement: continuum framework for constitutive modelling – Data repository

Gerrit Meijer, David Muir Wood, Jonathan Knappett, Glyn Bengough & Teng Liang
This dataset contains all data underlying the work presented in the linked Geotechnique journal publication. It contains the result of all experimental work described, as well as all numerical code (mixture of MATLAB, Python and R code) and numerical predictions for all computational models described.

Registration Year

  • 2021
    45

Resource Types

  • Image
    31
  • Dataset
    11
  • Text
    2
  • Interactive Resource
    1

Affiliations

  • University of Dundee
    13
  • National Taiwan University Hospital
    3
  • University of Maryland, Baltimore
    3
  • National Taiwan University
    3
  • Sunnybrook Hospital
    2
  • University of Zurich
    2
  • University College London
    2
  • École Polytechnique Fédérale de Lausanne
    2
  • University of Toronto
    2
  • European Molecular Biology Laboratory
    2