10 Works

The Ndc80 complex targets Bod1 to human mitotic kinetochores

Jason Swedlow & Katharina Schleicher

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. 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...

Common genetic variation drives molecular heterogeneity in human iPSCs

Helena Kilpinen, Angela Goncalves, Andreas Leha, , Sofie Ashford, , Dalila Bensaddek, Francesco Paolo Casale, Oliver Culley, Petr Danacek, Adam Faulconbridge, Peter Harrison, Davis McCarthy, Shane A McCarthy, Ruta Meleckyte, Yasin Memari, Nathalie Moens, Filipa Soares, Ian Streeter, , Alex Alderton, Rachel Nelson, Sarah Harper, Minal Patel, Laura Clarke … & Daniel J Gaffney
Our study provides a comprehensive picture of the major sources of genetic and phenotypic variation in iPSCs and establishes their suitability for use in genetic studies of complex human traits and cancer. Using a combination of genome-wide analyses we find that 5-25% of the variation in different iPSC phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. We also assess the phenotypic effects of rare, genomic copy number mutations that are recurrently...

Ardler Inventor Days Data

Loraine Clarke & Nick Taylor
Anonymised data collected from three Ardler Inventor Day events held as part of the EPSRC Hacking for Situated Civic Engagement projects. The dataset includes transcripts of interviews held with participants after each event

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...

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...

Quantitative 3D-Imaging for Cell Biology and Ecology of Environmental Microbial Eukaryotes

Sébastien Colin, Luis Pedro Coelho, Shinichi Sunagawa, Chris Bowler, Eric Karsenti, Peer Bork, Rainer Pepperkok & Colomban de Vargas
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.

Recorded Observation in Care Homes from BESiDE Study

Lesley J. McIntrye & Ian Ruaraidh Harrison
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,...

Systematic morphological profiling of human gene and allele function via Cell Painting

Mohammad H Rohban, , , Julia B Berthet, , , , Jesse S Boehm & Anne E Carpenter
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...

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