Briefly, when the relative abundance of a given cell type varies from sample to sample, measured expression levels of genes expressed in this cell type co-vary with the size of this cell population.
Since mucus accumulation in CF crypts appeared to be increased by lubiprostone treatment, we also measured expression levels of the two major mucin genes expressed in the small intestine, Muc2 and Muc3.
To assess radiation-induced response of protein markers in human lymphocytes irradiated ex vivo, we measured expression levels of our three best candidates, FDXR, DDB2 and ACTN1 protein, 3 days after initial exposure (Fig. 4B).
We also measured expression levels of classical HLA genes in eight HLA homozygous reference cell lines at baseline and after three treatments (heat shock, LPS, and IFN-gamma).
We next measured expression levels of pro-inflammatory cytokines interleukin 1 beta (IL-1β) and tumor necrosis factor alpha (TNF-α) by ELISA (Supplementary Fig. S1e f), but levels were unchanged in the NSC group (IL-1β; p = 0.4082 and TNF-α; p = 0.2115; NSC vs. sham), suggesting that NSCs modulated microglia function independent of these pro-inflammatory mediators.
Measured expression levels are all relative to these references.
To test this idea, we measured expression levels of VEGFA in Ire1α−/− MEFs transfected with mouse processed-XBP1 plasmid.
To determine whether PERK signaling is involved in WFS1 upregulation by valproate, we measured expression levels of phosphorylated eIF2α, which reflect PERK activation levels.
To validate our results, we measured expression levels of RSAD2 in a second independent group of patients (n = 30) before and after IFNß treatment.
We measured expression levels across three tissues (liver, cerebral cortex, skeletal muscle) for all eight genes for humans and chimpanzees (two individuals per species).
We measured expression levels of ubiquitin-activating enzyme E1A/E1B, ubiquitin-conjugating enzyme Ubc H7, ubiquitin C-terminal hydrolase and two p53-related E3 ligases, human papillomavirus E6-associated protein and mouse double minute 2 homolog.
