Selected article for: "cell type and expression analysis"
Author: Satria P. Sajuthi; Peter DeFord; Nathan D. Jackson; Michael T. Montgomery; Jamie L. Everman; Cydney L. Rios; Elmar Pruesse; James D. Nolin; Elizabeth G. Plender; Michael E. Wechsler; Angel CY Mak; Celeste Eng; Sandra Salazar; Vivian Medina; Eric M. Wohlford; Scott Huntsman; Deborah A. Nickerson; Soren Germer; Michael C. Zody; Gonçalo Abecasis; Hyun Min Kang; Kenneth M. Rice; Rajesh Kumar; Sam Oh; Jose Rodriguez-Santana; Esteban G. Burchard; Max A. Seibold
Title: Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium
  • Document date: 2020_4_10
    • ID: mj8ebo7i_36
    Snippet: As with the nasal brushing scRNA-seq data, 10X scRNA-seq data from ALI cultures 829 grown from a single tracheal donor that were either mock-or IL-13 stimulated for 10 830 days were pre-processed using Cell Ranger (version 3.0, 10X Genomics). To safeguard 831 against doublets, we removed all cells with gene or UMI counts exceeding the 99th 832 percentile. We also removed cells expressing fewer than 1,500 genes or for which > 833 populations, whic.....
    Document: As with the nasal brushing scRNA-seq data, 10X scRNA-seq data from ALI cultures 829 grown from a single tracheal donor that were either mock-or IL-13 stimulated for 10 830 days were pre-processed using Cell Ranger (version 3.0, 10X Genomics). To safeguard 831 against doublets, we removed all cells with gene or UMI counts exceeding the 99th 832 percentile. We also removed cells expressing fewer than 1,500 genes or for which > 833 populations, which we visualized in two dimensions using UMAP (see Figure 3d ). These 847 clusters were assigned cell type labels based their most upregulated genes, which were 848 identified by carrying out differential expression analysis between each cluster and all 849 others using Seurat's logistic regression (LR) test, in which cell treatment was included 850 as a latent variable. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.09.034454 doi: bioRxiv preprint rs18160331 and other variants is discretely divided into five quantiles and mapped into 1192 five colors (dark blue, sky blue, green, orange, and red) sequentially from low LD to high 1193

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