1,721,346 research outputs found
VEP predictions for ClinVar and gnomAD variants
No full textVariant effect predictions and DMS data for ClinVar and gnomAD variants in BRCA1, P53, CALM1, PTEN, HRAS and TPK1.Livesey, Benjamin. (2020). VEP predictions for ClinVar and gnomAD variants, [dataset]. MRC Human Genetics Unit. University of Edinburgh. https://doi.org/10.7488/ds/2799
Auxin-degron system identifies immediate mechanisms of Oct4
No full textMouse ESCs and iPSCs in which Oct4 could be depleted were analysed at different times following removal of Oct4 for changes in gene expression by RNA sequencing, in their epigenetic landscape by H3K27ac ChIP sequencing, and in Nanog binding by Nanog ChIP sequencing.Bates LE, Alves MRP, Silva JCR. Auxin-degron system identifies immediate mechanisms of OCT4. Stem Cell Reports 2021 Jul 13;16(7):1818-1831. PMID: 3414397
Genome-wide p-values of nine multivariate IgG glycan GWAS
No full textWhole-genome multivariate association results for nine groups of IgG N-glycosylation phenotypes. For the detailed definition of the glycan groups, please refer to Shen et al. (2017) Nature Communications: "Multivariate discovery and replication of five novel loci associated with Immunoglobulin G N-glycosylation".Shen, Xia. (2017). Genome-wide p-values of nine multivariate IgG glycan GWAS, [dataset]. University of Edinburgh. Institute of Genetics & Molecular Medicine (IGMM). http://dx.doi.org/10.7488/ds/2069
Community health worker-based mobile health (mHealth) approaches for improving management and caregiver knowledge of common childhood infections: A systematic review
No full textMahmood, Hana. (2020). Community health worker-based mobile health (mHealth) approaches for improving management and caregiver knowledge of common childhood infections: A systematic review, [dataset]. NIHR Global Health Research Unit on Respiratory Health (RESPIRE), Usher Institute, The University of Edinburgh
SUPERSEDED - GWAS summary statistics pertaining to the publication "Same role but different actors: genetic regulation of post-translational modification of two distinct proteins"
No full text## This item has been replaced by the one which can be found at https://datashare.ed.ac.uk/handle/10283/4088 ## Post-translational modifications (PTMs) diversify protein functions and dynamically coordinate their signalling networks, influencing most aspects of cell physiology. Nevertheless, their genetic regulation or influence on complex traits is not fully understood. Here, we compare for the first time the genetic regulation of the same PTM of two proteins – glycosylation of transferrin and immunoglobulin G (IgG). By performing genome-wide association analysis of transferrin glycosylation, we identified 10 significantly associated loci, all novel. Comparing these with IgG glycosylation-associated genes, we note protein-specific associations with genes encoding glycosylation enzymes (transferrin - MGAT5, ST3GAL4, B3GAT1; IgG - MGAT3, ST6GAL1) as well as shared associations (FUT6, FUT8). Colocalisation analyses of the latter suggest that different causal variants in the FUT genes regulate fucosylation of the two proteins. We propose that they affect the binding of different transcription factors in different tissues, with fucosylation of IgG being regulated by IKZF1 in B-cells and of transferrin by HNF1A in liver.Landini, Arianna. (2021). GWAS summary statistics pertaining to the publication "Same role but different actors: genetic regulation of post-translational modification of two distinct proteins", [dataset]. University of Edinburgh. College of Medicine and Veterinary Medicine. Usher Institute. https://doi.org/10.7488/ds/316
Cornea resistance factor GWAS in the UK Biobank
No full textSummary statistics from the genome-wide association study (GWAS) of cornea resistance factor (CRF) of 76,029 UK Biobank samples of British ancestry obtained through the application number 19655. The CRF analysis was performed on the average of the left and right eye measurements. Any outliers (i.e. CRF greater than population mean difference + 3 standard deviations) were removed. Further phenotypic filtering was applied by removing samples linked to, or self-reporting, ocular conditions that could affect the measurements accuracy such as eye surgery, refractive laser surgery, cataract surgery, glaucoma high pressure surgery or laser treatment, corneal graft surgery, eye injury , keratoconus or cornea disorders. A total of 102490 samples were kept. Using the genetic quality control of the UK Biobank the 76318 samples of British ancestry with imputed data failing heterozygosity or/and missingness, or having a mismatch between self-reported and genotype-derived gender or showing putative sex chromosome aneuploidy as well as individuals who have withdrawn from the study at the time of analysis were removed. An total of N-76029 were included in the GWAS. The GWAS was performed on common and low-frequency (MAF > 0.5%) well imputed (INFO > 0.6) variants using a linear mixed model accounting for population structure and (cryptic) relatedness, implemented in the software BOLT_LMM v1.3. Covariates fitted in the model were: age, sex, assessment centre, genotyping array, genotyping batch and the 20 first principal components of ancestry provided by the UK Biobank.Boutin, Thibaud. (2020). Cornea resistance factor GWAS in the UK Biobank, [dataset]. https://doi.org/10.7488/ds/294
J-Baxter/foundervariantsHIV_prognosismodelling: v1.0.0
No full textNo description provided.James Baxter. (2024). J-Baxter/foundervariantsHIV_prognosismodelling: v1.0.0 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.1371145
EBV serostatus and total number of siblings GWAS summary statistics
No full textGWAS on EBV serostatus/total number of siblings on UKBiobank participants Mendelian randomisation identifies priority groups for prophylactic EBV vaccination. Marisa D. Muckian, MSc; James. F Wilson, DPhil; Graham S. Taylor, PhD; Helen R. Stagg, PhD; Nicola Pirastu, PhD We mapped the complex evidence from the literature prior to this study factors associated with EBV serostatus (as a proxy for infection) into a causal diagram to determine putative risk factors for our study. Using data from the UK Biobank of 8,422 individuals genomically deemed to be of white British ancestry between the ages of 40 and 69 at recruitment between the years 2006 and 2010, we performed a genome wide association study (GWAS) of EBV serostatus and total number of sibligns, followed by a Two Sample MR to determine which putative risk factors were causal
An in vitro - agent-based modelling approach to optimisation of culture medium for generating muscle cells: Live images
No full textLive image data used in the study "An in vitro - agent-based modelling approach to optimisation of culture medium for generating muscle cells". Live imaging was performed using an inverted microscope (Zeiss Cell Observer SD or Zeiss Cell observer) in widefield mode, using a 20x phase air objective (Plan-Apochromat Ph2 NA 0.80 or EC Plan-Neofluar Ph 2 NA 0.50, respectively). Cells were imaged 2 hours after adding the respective differentiation medium. 3x3 tiles with 10% overlap with 2x2 binning were taken every 5 minutes for a minimum of 12 hours. Images were stitched using Zen Blue software and stacked into 30 minutes videos for further quantitative analysis.ions.Hardman, David. (2022). An in vitro - agent-based modelling approach to optimisation of culture medium for generating muscle cells: Live images, [moving image]. University of Edinburgh. Usher Institute. https://doi.org/10.7488/ds/3435
Optical Coherence Tomography Angiography retinal scans and segmentations
No full textOptical Coherence Tomography Angiography retinal scans from 11 participants in the PREVENT study and associated manual segmentations of the vasculature in the scans. Optical coherence tomography angiography (OCTA) is a novel non-invasive imaging modality for the visualisation of microvasculature in vivo. OCTA has encountered broad adoption in retinal research. OCTA potential in the assessment of pathological conditions and the reproducibility of studies relies on the quality of the image analysis. However, automated segmentation of parafoveal OCTA images is still an open problem in the field. In this study, we generate the first open dataset of retinal parafoveal OCTA images with associated ground truth manual segmentations. Imaging was performed using the commercial RTVue-XR Avanti OCT system (OptoVue, Fremont, CA). Consequent B-scans, each one consisting of 304×304 A-scans, were generated in 3×3 mm field of view centered at the fovea. In this work, we selected images only of the superficial layer (containing the vasculature enclosed in the internal limiting membrane layer (ILM) and the inner plexiform layer (IPL)) from left and right eyes of 11 participants with and without family history of dementia as part of a prospective study aimed to find early biomarkers of neurodegenerative diseases (PREVENT). For each of those images we extracted five subimages, one from each clinical region of interest (ROI): superior, nasal, inferior, temporal, and fovea. Poor quality ROIs were discarded and from the remaining a dataset containing 55 ROIs was created.Giarratano, Ylenia. (2019). Optical Coherence Tomography Angiography retinal scans and segmentations, [image]. University of Edinburgh. Medical School. https://doi.org/10.7488/ds/2729
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