The dataset shown represents a timelapse sequence showing cell and tissue dynamics during primitive streak formation in chick embryo. The data were acquired using Myr-GFP embryos and a custom built light-sheet microscope. The sequence shows the developmental period covering the time interval from the freshly laid egg (stage EGXIII), prior to the onset of tissue movement until the end of the formation of the primitive streak (Stage HH4). Shown here is only one of the...

Long noncoding RNAs (lncRNAs) regulate many biological processes and have been implicated in development and disease pathogenesis. The exact function for the large majority of lncRNAs is still unknown. To address whether lncRNAs could play a role in cell division, we combined a microscopy-based high-content RNAi screen with dedicated image analysis workflows to identify lncRNAs that regulate mitotic progression, chromosome segregation and cytokinesis. By targeting over 2000 lncRNAs in HeLa cells, we discovered an assortment...

Screen Description Primary image-based screen of 1,278 mostly FDA-approved, off-patent small molecules, collected in the Prestwick Chemical Library for inhibitors of Human adenovirus infection

Screen Description Human adenovirus infected Z' plates in biological duplicates consisting of 192 technical replicates of the solvent control DMSO and positive control DFT to confirm assay quality

Comparison of whole-mouse brain data acquired from a CLARITY-cleared VIP-tdTomato mouse with and without ASLM mode engaged

Social Printers were a network of devices that allowed users to send messages that would be printed out on every device. These were given to households during the Scottish Elections 2016 and the EU Referendum 2016, who used them for anonymous discussion during political television programming. This dataset comprises the messages that were sent and interviews conducted with participants before and after the study. This work was carried out by Katerina Gorkovenko as part of...

50 Salads Activity recognition research has shifted focus from distinguishing full-body motion patterns to recognizing complex interactions of multiple entities. Manipulative gestures - characterized by interactions between hands, tools, and manipulable objects - frequently occur in food preparation, manufacturing, and assembly tasks, and have a variety of applications including situational support, automated supervision, and skill assessment. With the aim to stimulate research on recognizing manipulative gestures we introduce the 50 Salads dataset. It captures 25...

Imaging a chicken embryo with the mesoSPIM

3D confocal live imaging of the zebrafish posterior lateral line primordium labeled with the membrane marker cldnB:lyn-EGFP for segmentation and optionally with one of several additional labels.

We have adapted the mouse kidney rudiment assay to generate renal organoids. 24 hours after pelleting 100,000 mouse kidney cells, organoids had formed in the PDMS dishes. For the PNA vital stain test we used kidney cells from wildtype mice and for the tracking time series we used cells from the Wt1tm1Nhsn strain, expressing GFP together with the transcription factor Wt1. One organoid was embedded in a hydrogel matrix (1.5% Agarose + 3% gelatine). In...

We use quantitative time-lapse microscopy combined with microfluidics to analyse the induction dynamics of the lac operon in single bacteria cells.

To identify possible candidates for progression towards clinical studies against SARS-CoV-2, we screened a well-defined collection of 5632 compounds including 3488 compounds which have undergone clinical investigations (marketed drugs, phases 1 -3, and withdrawn) across 600 indications. Compounds were screened for their inhibition of viral induced cytotoxicity using the human epithelial colorectal adenocarcinoma cell line Caco-2 and a SARS-CoV-2 isolate. The primary screen of 5632 compounds gave 271 hits. A total of 64 compounds with...

Our ability to understand the genotype-to-phenotype relationship is hindered by the lack of detailed understanding of phenotypes at a single-cell level. To systematically assess cell-to-cell phenotypic variability, we combined automated yeast genetics, high-content screening and neural network-based image analysis of single cells, focussing on genes that influence the architecture of four subcellular compartments of the endocytic pathway as a model system. Our unbiased assessment of the morphology of these compartments — endocytic patch, actin patch,...

Our ability to understand the genotype-to-phenotype relationship is hindered by the lack of detailed understanding of phenotypes at a single-cell level. To systematically assess cell-to-cell phenotypic variability, we combined automated yeast genetics, high-content screening and neural network-based image analysis of single cells, focussing on genes that influence the architecture of four subcellular compartments of the endocytic pathway as a model system. Our unbiased assessment of the morphology of these compartments — endocytic patch, actin patch,...

Nucleocytoplasmic transport is tightly regulated by the nuclear pore complex (NPC). Even very large cargoes such as many pathogens, mRNAs and pre-ribosomal subunits can pass the NPC intact. Compared to small import complexes, for such large cargoes >15 nm there is very little quantitative understanding of the mechanism for efficient transport, the role of multivalent binding to nuclear transport receptors via nuclear localisation sequences (NLSs) and effects of size differences. Here, we assayed nuclear import...

3D confocal imaging of fixed samples of the zebrafish posterior lateral line primordium labeled with the membrane marker cldnB:lyn-EGFP and stained for pea3 mRNA using single molecule Fluorescence In-Situ Hybridization (smFISH).

The intestinal epithelium maintains an important barrier throughout life. It consists of several epithelial cell lineages that are derived from LGR5+ intestinal stem cells. Although epigenetic regulation of embryonic stem cell differentiation is well established, its role in adult stem cell systems such as the intestinal epithelium is still undefined. Yet, targeting of epigenetic regulatory enzymes may be relevant for new therapeutics, for example in cancer treatment. Here, we combine a newly established organoid toolbox...

Gene expression studies in early human development from 3 to 17 post conceptional weeks (PCW).

Recording of daily life experiences from a first-person perspective has become more prevalent with the increasing availability of wearable cameras and sensors. This dataset was captured during development of a system for automatic detection of social interactions in such data streams, and in particular focused interactions in which co-present individuals, having mutual focus of attention, interact by establishing face-to-face engagement and direct conversation. Existing public datasets for social interaction captured from first person perspective tend...

Cardiac histopathology from human patients with clinical heart failure or cadaveric donor hearts from patients without clinical heart failure. Human tissue research: Human heart tissue was procured from two separate groups of subjects: heart transplant or LVAD recipients with severe heart failure (Fal), and brain dead, organ donors with no history of heart failure (non-failing, NF). Tissue from patients with ischemic cardiomyopathy sampled infarct-free regions. No organs or tissue were procured from prisoners. Prospective informed...

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...

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...