Scientists discover key 'culprits' in major lungcancer study NatureComms
function was then used to calculate per-cell expression levels for fibroblast and mural cell gene signatures and fibroblasts were identified as those cells where the fibroblast signature score - mural cell signature score >0.1 and the fibroblast signature score >0.
A consensus list of fibroblast genes was then identified as those expressed in >1% of fibroblasts in each dataset. The Seurat packagefunction was then used to calculate rPCA corrected expression values for these consensus fibroblast genes within each dataset.The fibroblasts isolated from each scRNA-seq datasets were integrated using canonical correlation analysis dimensionality reduction to create a shared low-dimensional space across datasets.
To infer differentiation trajectories, we used the destiny R package to perform diffusion map dimensionality reduction, cluster cells by diffusion pseudotime branches and calculate pseudotime values. A loess regression model was then used to identify genes that were differentially expressed in and calculate fitted values for each gene’s expression profile in pseudotime for each dataset, using the gam R package.
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Fibroblast A20 governs fibrosis susceptibility and its repression by DREAM promotes fibrosis in multiple organs - Nature CommunicationsA20 gene variants are linked with systemic sclerosis (SS), but the mechanisms are unclear. Here, the authors show that A20 expression is reduced in SS skin and lungs, that its ablation in mice induces SS, and that show that fibrosis can be ameliorated by induction of A20.
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Blueprint to reverse nature's decline revealedMinisters set out plans for restoring nature amid growing criticism over pollution and wildlife decline.
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Thérèse Coffey: Nature is being forgotten in the climate change debate'Nature needs us to accelerate our help if we want to enjoy it for generations to come.' ✍️ theresecoffey for ipaperviews
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Single-cell T cell receptor sequencing of paired human atherosclerotic plaques and blood reveals autoimmune-like features of expanded effector T cells - Nature Cardiovascular ResearchDepuydt and Schaftenaar et al. profile the T cell clonality in patients with atherosclerosis by performing single-cell T cell receptor sequencing on carotid artery plaques and matched peripheral blood mononuclear cell samples. The analyses showed plaque-specific clonal expansion in effector CD4+ T cells, expressing genes indicative of exposure to activating antigens, thus suggesting that atherosclerosis has an autoimmune component driven by autoreactive CD4+ T cells.
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Miley Cyrus prompts massive boost in flower sales at Lidl thanks to new singleMiley Cyrus (MileyCyrus) has seemingly caused a boom in Lidl's flower sales - which is extremely iconic 🌹 😍
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