Extended Data Fig. 4: Gene expression profiles of L2ox and L2red. | Nature

Extended Data Fig. 4: Gene expression profiles of L2ox and L2red.

From: Developmental ROS individualizes organismal stress resistance and lifespan

Extended Data Fig. 4

a, Steady-state transcript levels of selected oxidative stress-related genes in L2ox and L2red worms. n, number of independent sorting experiments; unpaired two-sided t-test. Data are mean ± s.e.m. b, Volcano plot showing fold changes versus P values for the transcriptomes of L2ox and L2red subpopulations. DEGs (P ≤ 0.05) are represented by red dots (see Methods for statistical definition of DEGs). Data were collected from four independent sorting experiments. c, GSEA of the 327 DEGs. Normalized enrichment scores (see Methods for calculation) are represented by the bar graph. Terms (for summary, see Supplementary Table 1) indicating origin, process or phenotype associated with genes known to have a role in the process are shown on the left. Some terms (*) have been merged and are represented as a single category bar for simplicity (for detailed values, see Supplementary Table 1). d, e, Percentage of DEGs identified in L2ox that intersect with H3K4me3 peak signals within their 5′ region (500 bp upstream and downstream from the transcription start site). The H3K4me3 chromatin immunoprecipitation (ChIP) datasets were generated from L3-staged N2 worms: ChIP chip, GEO entry GSE30789 in d and chromatin immunoprecipitation followed by sequencing (ChIP–seq), GEO entry GSE28770 in e, indicating that these marks are set during larval development. Hypergeometric probability: d, P = 0.064; e, P = 2.786 × 10−6. In f, g, Venn diagrams show the overlap among upregulated (f) or downregulated (g) gene sets in L2ox and downregulated or upregulated set-9(rw5) and set-26(tm2467) gene sets (GEO entry: GSE100623). See Supplementary Table 1 for datasets in dg.

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