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. 2019 Feb 20;9:2324. doi: 10.1038/s41598-019-39112-6

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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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Time-resolved transcriptomic analysis of HSC activation. (A) Log₂FC for all expressed genes in WD, CCl₄, and IVT experiments relative to controls (log₂CPM >2). Induced and repressed genes (FDR ≤0.05), shown in red and blue, respectively. Gene numbers are indicated. (B) Distance plot and k-means clustering of all samples of the three experiments based on genes differentially expressed (FDR ≤0.01) between HSCs from 24w WD- and chow-fed mice. (C) 870 common genes induced ≥4-fold (FDR <0.05), between any two time points in all three experiments, or repressed ≥4-fold (FDR <0.05). (D) Common genes clustered by profiles of variance-stabilized, scaled exon counts through WD and CCl₄ experiments. Gene counts and mean aggregate profiles are shown (bold line). Pearson’s correlation coefficient of mean aggregate profiles are shown for cluster pairs. Middle panel bean plots show normalized log₂(RPKM) values and medians for each WD cluster. Dashed lines show average log₂(RPKM) values across time course. (RPKM: Reads Per Kilobase of transcript per Million mapped reads). (E) Exon counts for 360 genes in WD clusters 1–7, which are shared with corresponding CCl₄ clusters. Number of shared genes in each cluster pair, percent of parent WD cluster, and cluster numbers (circles) are shown. (F) Enriched (green; FDR ≤0.01) go-slim categories and -log₁₀(FDR) values for each WD cluster. Common genes expressed at RPKM ≥10 at any time point in the three experiments are included in the go-analysis. Density strip plots show distributions and median log₂FC values (24w WD vs. chow) for genes of enriched go-slim categories within respective clusters. All values are averages of 3–4 biological replicates.