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. 2019 Jul 3;9:9580. doi: 10.1038/s41598-019-45842-4

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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In vitro culture alters fibroblast transcriptomes. (a) Volcano plot of genes differentially expressed (log(fold change) >1) between in vitro and ex vivo fibroblasts. Genes selected for analysis at real time-PCR are highlighted in red. (b) Dendrogram showing unsupervised hierarchical clustering of average gene expression for the four cell populations. (c–g) Dot plots showing changes in gene expression (real-time PCR) in primary lung fibroblasts following culture on plastic or in 3D (collagen:Matrigel gels): (c) ACTA2, (d) COL1A1, (e) COL3A1, (f) IL6, (g) CFD and (h) MGP. Gene expression levels expressed as the log2 fold change relative to mean expression across all samples (n = 4). ▲: NOF, ♦: CAF. *p < 0.05, ***p < 0.001, ****p < 0.0001, unpaired or Welch’s t-tests. Further data associated with this figure can be found in Figs S7–S9.