Extended Data Fig. 3: Attenuated IFN-γ and T-bet response in CD4+ T cells of STIM1 deficient patient.
a, mRNA levels of IFNG, IL2 and TNF in CD4+ T cells from the patient (PT), his father (Fa), mother (Mo) and a HD stimulated with anti-CD3/28 for 6 hours and analyzed by RNA-seq. b, Metascape analysis of all downregulated differentially expressed genes (DEGs) in HD, Fa, Mo vs. the PT. c, IPA upstream regulator analysis of DEGs in CD4+ T cells from the PT vs. all three controls (HD, Fa and Mo) ranked by P value and separated by upstream signaling molecules and transcription factors. Colors indicate the activation Z score. d, Epigenetic Landscape In Silico deletion Analysis (LISA) of transcriptional regulators of downregulated DEGs in T cells from the PT vs. all three controls (HD, Fa and Mo) ranked by P value. Note that LISA uses different ChIP-Seq datasets to identify transcriptional regulators; T-bet is identified as ‘T’ using GSE81881 (human Th1 cells) indicated here as T-bet*, and as Tbx21 using GSE33802 (mouse Th1 cells) indicated as Tbx21#. Fold changes were shrunk using the apeglm method. DEGs were considered significant if shrinkage of the log2 fold change (LFC) absolute value was > 0.5, and the adjusted P value < 0.05.
