Figure 3—figure supplement 1. | Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence

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Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence

Figure 3—figure supplement 1.

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Joslin Diabetes Center, United States; Harvard Medical School, United States; Boston University, United States
Figure 3—figure supplement 1.
Download figureOpen in new tabFigure 3—figure supplement 1. Gene expression changes following GSC inhibition.

(A) qRT-PCR validation of RNA samples used for RNA-seq. gst-4 and nit-1 are direct SKN-1 targets (Robida-Stubbs et al., 2012). Data are represented as mean ± SEM. n = 3; p < 0.05*. Analysis of a different RNA sample set is shown in Figure 2D. (B) DAVID analysis of genes that were downregulated in glp-1(ts). Processes related to GSC maintenance and reproduction were highly represented, as expected. (C) Altered abundance of tissue-specific genes in GSC(−) animals. Adult hermaphrodite worms have 959 somatic cells and ∼2000 GSCs (Kimble and Crittenden, 2005). A representative somatic-specific gene would therefore be predicted to be present at higher relative abundance in GSC(−) samples after normalization to either total RNA or reference housekeeping genes. Accordingly, representative somatic tissue-specific genes (Richmond, 2005; Moerman and Williams, 2006; Chikina et al., 2009) were present at threefold to fourfold higher relative levels in the GSC(−) samples. By contrast, a germline-specific gene (efl-1) was underrepresented (∼4×) in GSC(−) samples. Reference genes that are ubiquitously expressed in all tissues and commonly used for qRT-PCR normalization (Hoogewijs et al., 2008) do not have altered relative abundance in the GSC(−) samples. (D, E) Frequency distribution plots of mRNA levels in glp-1(ts) worms relative to wild type. A cutoff of FC > 4 denotes 1,306 out of 12,595 genes sequenced (10.4%).

DOI: http://dx.doi.org/10.7554/eLife.07836.008