Hela cells were transfecetd with the human Lincode small interfering RNA (siRNA) library targeting 2231 lncRNAs. Following 48 hr incubation, cells were fixed and processed for immunostaining and subsequent automated image acquisition and analysis. In screen B, phospho-histone H3 (PHH3; to specifically label mitotic cells), alpha-tubulin, gamma-tubulin (to label centrosomes) and Hoechst was used. 10x 384-well plates were used. The fixation and staining for both screen A and B was carried out at the Institute...

eHCFM: a 3D-fluorescence imaging and classification tool for high throughput analysis of microbial eukaryotes in environmental samples. The methods generates for each given sample a mosaic of multi-dimentional fields of view (3D, 5 channels). We propose here the exploration of raw images of plankton samples from the Tara Oceans expeditions.

This data-set contains information of recorded ethnographic observations (utilising an adapted form of the AEIOU heuristic) from five urban care homes in the UK. These observations are formatted in both transcribed and coded tables and as scans of original field notes. The data set includes method statements describing the process of data capture. Affinity mapping was employed to open-code the data and develop a code book. Five high-level spatial qualities emerged: Spatial Legibility, Spatial Interconnectedness,...

We hypothesized that human genes and disease-associated alleles might be systematically functionally annotated using morphological profiling of cDNA constructs, via a microscopy-based Cell Painting assay. Indeed, 50% of the 220 tested genes yielded detectable morphological profiles, which grouped into biologically meaningful gene clusters consistent with known functional annotation (e.g., the RAS-RAF-MEK-ERK cascade). We used novel subpopulation-based visualization methods to interpret the morphological changes for specific clusters. This unbiased morphologic map of gene function revealed TRAF2/c-REL...

The Edible Plant Database (EPD) is an outcome of the GROW Observatory, a European Citizen Science project on growing food, soil moisture sensing and land monitoring. This dataset was disseminated via a web service hosted by IIASA (Austria) that provides information about suitable plants for locations within Europe, based on climate. The web service was used in the GROW app, this dataset is the base information used for that service. Key growing data, for example,...

COVID-19, caused by the SARS-CoV-2 virus, is a flu-like disease with a respiratory route of transmission, yet clinical evidence suggests that the intestine may present another viral target organ. Indeed, the SARS-CoV-2 receptor ACE2 (angiotensin converting enzyme 2) is highly expressed on differentiated enterocytes. In human small intestinal organoids, enterocytes were readily infected by SARS-CoV and SARS-CoV2 as demonstrated by confocal- and electron-microscopy. Consequently, significant titers of infectious viral particles were measured. mRNA expression analysis...

Multiplexed imaging of breast cancer tissues for 37 proteins

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,...

In higher plants, germline differentiation occurs during a relatively short period within developing flowers. Understanding of the mechanisms that govern germline differentiation lags behind other plant developmental processes. This is largely because the germline is restricted to relatively few cells buried deep within floral tissues, which makes them difficult to study. To overcome this limitation, we have developed a methodology for live imaging of the germ cell lineage within floral organs of Arabidopsis using light...

Here we use 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify linked chromatin domains (CDs) composed of irregular ~200-300-nm-wide aggregates of nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin region. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications towards the core of CDs in both hetero- and...

Here we use 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify linked chromatin domains (CDs) composed of irregular ~200-300-nm-wide aggregates of nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin region. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications towards the core of CDs in both hetero- and...

Here we use 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify linked chromatin domains (CDs) composed of irregular ~200-300-nm-wide aggregates of nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin region. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications towards the core of CDs in both hetero- and...

Myelin is an essential component of the nervous system and myelin damage causes demyelination diseases. Myelin is a sheet of oligodendrocyte membrane wrapped around the neuronal axon. In the fluorescent images, experts manually identify myelin by co-localization of oligodendrocyte and axonal membranes that fit certain shape and size criteria. Because myelin wriggles along x-y-z axes, machine learning is ideal for its segmentation. However, machine-learning methods, especially convolutional neural networks (CNNs), require a high number of...

Predicting gene expression from DNA sequence remains a major goal in the field of gene regulation. A challenge to this goal is the connectivity of the network, whose role in altering gene expression remains unclear. Here, we study a common autoregulatory network motif, the negative single-input module, to explore the regulatory properties inherited from the motif. Using stochastic simulations and a synthetic biology approach in E. coli, we find that the TF gene and its...

Method validation data generated as part of quantifying the measurement uncertainty of delta-9-tetrahydrocannabinol (THC, the main active ingredient of cannabis) in whole Blood using SPE and LC/MS/MS Key words calibration curve, coverage factor, method validation, method precision, standard solution

Predicting gene expression from DNA sequence remains a major goal in the field of gene regulation. A challenge to this goal is the connectivity of the network, whose role in altering gene expression remains unclear. Here, we study a common autoregulatory network motif, the negative single-input module, to explore the regulatory properties inherited from the motif. Using stochastic simulations and a synthetic biology approach in E. coli, we find that the TF gene and its...

This dataset contains the semen parameters of a fertile man, who have achieved a pregnancy in ≤ 12 months of trying to conceive, with an abstinence period of 2-7 days, at time of semen analysis. The parameters of a semen analysis included are; Semen Volume (ml), Sperm concentration(10x6 per ml), Total sperm number (10x6 per ejaculate), Total motility (PR + NP, %), Progressive motility (PR, %), Non-progressive motility (NP, %), Immotile spermatozoa (IM, %), Vitality...

Lighter fuel samples from five different commercial sources were purchased. Samples of 10, 25, 50, 75, 90, and 95% evaporated product were prepared, resulting in 40 samples in total which were analyzed using gas chromatography–mass spectrometry.

We performed single molecule in-situ hybridization on yeast cells that have been exposed to osmotic stress and measured mRNA expression for two genes. The goal of this study was to generate data sets for single cell transcription modeling.

Petrol samples were collected directly from nine different public fuelling stations in Glasgow, Scotland. Samples of 10, 25, 50, 75, 90, and 95% evaporated product were prepared, resulting in 63 samples in total which were analyzed using gas chromatography–mass spectrometry.

Genome-edited cells with homozygously mEGFP-tagged Condensin subunits and chromosomes stained by SiR-DNA were imaged every 90 s for a total of 60 min by 3D confocal microscopy, which was automatically triggered after prophase onset. Images were calibrated by FCS to convert fluorescence intensities into cellular protein concentration maps and cellular protein number maps.

Characterization of cytoskeletal systems (actin, microtubules, vimentin networks) to cyclic straining using confocal laser scanning microscopy, including experiments with nocodazole to depolymerize microtubules.

Methods for measuring the properties of individual cells within their native 3D environment will enable a deeper understanding of embryonic development, tissue regeneration, and tumorigenesis. However current methods for segmenting nuclei in 3D tissues are not designed for situations where nuclei are densely packed, non- spherical, heterogeneous in shape, size, or texture, all of which are true of many embryonic and adult tissue types as well as in many cases for cells differentiating in culture....