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Editorial
. 2020 Dec 1;319(6):L887-L893.
doi: 10.1152/ajplung.00451.2020. Epub 2020 Sep 30.

The Idiopathic Pulmonary Fibrosis Cell Atlas

Nir Neumark  1   2 , Carlos Cosme Jr  1 , Kadi-Ann Rose  1 , Naftali Kaminski  1
Affiliations
Editorial

The Idiopathic Pulmonary Fibrosis Cell Atlas

Nir Neumark et al. Am J Physiol Lung Cell Mol Physiol. .
No abstract available

Keywords: IPF; data sharing; single-cell RNAseq; systems biology.

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Conflict of interest statement

N.K. served as a consultant to Biogen Idec, Boehringer Ingelheim, Third Rock, Pliant, Samumed, NuMedii, Theravance, LifeMax, Three Lake Partners, Optikira, and Astra Zeneca over the last 3 years, reports equity in Pliant, a grant from Veracyte, and nonfinancial support from MiRagen and Astra Zeneca, and has intellectual property on novel biomarkers and therapeutics in IPF licensed to Biotech. None of the other authors has any conflicts of interest, financial or otherwise, to disclose.

Figures

Fig. 1.
Fig. 1.
Flowchart of the IPF Cell Atlas gene search and plot generation pipeline. Briefly, a user will input a gene into the gene search box provided in all analysis tools and will click the search button after toggling the tool-specific plotting options. The website then runs a query of our gene expression-containing database to selectively pull out the data for the input gene. The expression data are appended to the cell metadata for a given data set before being run through R code from the ggplot2 package to output the figure.
Fig. 2.
Fig. 2.
Screenshots of analysis tools that are available on the IPF Cell Atlas website. A: UMAP Explorer feature that allows the user to visualize gene expression of an input gene within a selected cell grouping (i.e., epithelial, immune, stromal, mesenchymal, immune; data set dependent) on a 2-dimensional UMAP projection clustered by cell type. B: Batch Explorer features that plot a dot plot of differential gene expression for up to 8 genes within a selected cell grouping. In addition to expression differences between control and IPF samples, the dot plot provides information on the average level of expression of each gene per cell type as well as the percentage of cells of that cell type expressing each gene. C: data set comparison tool for comparing gene expression on the different UMAPs generated for each of the data sets. D: Gene Explorer feature that allows a user to input a gene and observe cell-specific differential expression patterns in a violin plot, bar graph, density plot, or box plot format. Users can toggle the type of plot and whether to display results that compare control to IPF.
Fig. 3.
Fig. 3.
Website usage statistics provided through Google Analytics. A: heatmap of unique users to the portal from across the globe. B: pie charts of the top 5 searched genes before the pandemic (November 2019) and during the pandemic (August 2020). Percentages shown represent the percentage of searches of that gene within the 5 genes shown. C: line graph displaying the number of unique users accessing the website each month since it was made public.
See this image and copyright information in PMC

References

    1. Adams TS, Schupp JC, Poli S, Ayaub EA, Neumark N, Ahangari F, Chu SG, Raby BA, DeIuliis G, Januszyk M, Duan Q, Arnett HA, Siddiqui A, Washko GR, Homer R, Yan X, Rosas IO, Kaminski N. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. Sci Adv 6: eaba1983, 2020. doi:10.1126/sciadv.aba1983. - DOI - PMC - PubMed
    1. Carraro G, Mulay A, Yao C, Mizuno T, Konda B, Petrov M, Lafkas D, Arron JR, Hogaboam CM, Chen P, Jiang D, Noble PW, Randell SH, McQualter JL, Stripp BR. Single cell reconstruction of human basal cell diversity in normal and IPF lung. Am J Respir Crit Care Med In press. doi:10.1164/rccm.201904-0792OC. - DOI - PMC - PubMed
    1. Habermann AC, Gutierrez AJ, Bui LT, Yahn SL, Winters NI, Calvi CL, Peter L, Chung MI, Taylor CJ, Jetter C, Raju L, Roberson J, Ding G, Wood L, Sucre JM, Richmond BW, Serezani AP, McDonnell WJ, Mallal SB, Bacchetta MJ, Loyd JE, Shaver CM, Ware LB, Bremner R, Walia R, Blackwell TS, Banovich NE, Kropski JA. Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis. Sci Adv 6: eaba1972, 2020. doi:10.1126/sciadv.aba1972. - DOI - PMC - PubMed
    1. Morse C, Tabib T, Sembrat J, Buschur K, Bittar H, Valenzi E, Jiang Y, Kass D, Gibson K, Chen W, Mora A, Benos P, Rojas M, Lafyatis R. Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis. Eur Respir J 54:1802441, 2019. doi:10.1183/13993003.02441-2018. - DOI - PMC - PubMed
    1. Raredon MS, Adams TS, Suhail Y, Schupp JC, Poli S, Neumark N, Leiby KL, Greaney AM, Yuan Y, Horien C, Linderman G, Engler AJ, Boffa DJ, Kluger Y, Rosas IO, Levchenko A, Kaminski N, Niklason LE. Single-cell connectomic analysis of adult mammalian lungs. Sci Adv 5: eaaw3851, 2019. doi:10.1126/sciadv.aaw3851. - DOI - PMC - PubMed

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