NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap(4)A) and Down-Regulates Immune Response and Cancer Promotion Genes

Marriott, Andrew S.; Vasieva, Olga; Fang, Yongxiang; Copeland, Nikki A.; McLennan, Alexander G.; Jones, Nigel J.

Supporting Information S1 Table. Primers used for qRT-PCR verification of RNA-Seq data. (DOCX) S2 Table. Raw data for the 31,177 reads mapped to the human reference genome. Data include Ensembl gene id, chromosome mapping data, log 2 counts per million mapped reads (CPM), log 2 fold changes for four contrasts, P-values and FDR-adjusted P-values, raw counts and individual sample and mean FPKM values. The table does not contain the genes with zero read counts in all libraries. (XLSX) S3 Table. List of the subset of 4,835 genes showing differential expression between KBM-7 and KBM-7-NuKO cells with fold-change 1.2 and P <0.05. Data include Ensembl and gene id, log 2 CPM, mean FKPM value of triplicate KO and WT samples, log 2 fold change, fold change (up-regulation in red, down-regulation in green), FDR-adjusted P-value and approved gene name. List includes unannotated genes, pseudogenes and some non-protein coding genes. (XLSX) S4 Table. Mapping of DEGs to Ingenuity1 canonical pathways. Data include the observed overall direction of regulation [down (-) or up(+)], -log 2 (P-value), z-score and key molecules in each pathway. (XLSX) S5 Table. DEGs from this study previously shown to be regulated by (A) Type I, (B) Type II and/or (C) Type III interferons according to the Interferome v2.01 database. Data include Ensembl id, gene id and description, and fold up-(red) or down-(green) regulation in this study. Genes potentially showing specific regulation by Type III IFNs are highlighted in yellow. (XLSX) S6 Table. Genes identified by IPA 1 to be associated with rheumatoid arthritis and systemic lupus erythematosus. Table. Upstream regulators predicted by IPA 1 . Data include the predicted upstream regulator, the direction of regulation with which it is associated (-down; + up), the type of molecule, the activation state (predicted direction of the biological function), the activation z-score, where >2.0 or <-2.0 is significantly predictive, the P-value and the molecules for which there is documented evidence for regulation. The top transcription factors examined in