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Supplementary Data SUPPLEMENTARY DATA Supplementary Figure 1. Expression of 84 genes associated with response to interferon extracted from RNA-seq data of isolated islets from subjects with recent T1D onset and islets from non-diabetic organ donors. The expression is displayed as fold up- or down regulation compared to the mean expression in the three non-diabetic controls. ©2016 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db16-0616/-/DC1 SUPPLEMENTARY DATA Supplementary Figure 2. Fold overexpression compared to controls of the ISGs in laser-captured T1D islets in this study (A) and what has been induced experimentally in isolated islets in other studies (B-E). The data in (B) was extracted from the RNA sequencing data of islets exposed to IL1 and IFN for 48 h, published by Eizirik et al. 2012 (1), Supporting information, Dataset S1, “table_RPKM.xls. The data in (C) and (D) were from microarray data on islets infected with Coxsackievirus B5 (C) or islets exposed to IL1 and IFN (D) for 48 h, published by Ylipaasto et al. 2005 (2), Electronic Supplementary Material 2 and 3. The data in (E) is from PCR array data of islets exposed to IFN for 6 h and published by Lind et al. 2013 (3), Supplemental file 1. In Ylipaasto et al, only genes considered significantly changed were reported and thus, in (C) and (D), genes that were not significantly changed are displayed as zero. Lind et al used an earlier version (QIAGEN, PAHS-016A) of the ISG PCR array used in this study (QIAGEN, PAHS-016ZC), and thus, only genes included in both arrays are shown in (E). 1. Eizirik DL, Sammeth M, Bouckenooghe T, Bottu G, Sisino G, Igoillo-Esteve M, Ortis F, Santin I, Colli ML, Barthson J, Bouwens L, Hughes L, Gregory L, Lunter G, Marselli L, Marchetti P, McCarthy MI, Cnop M: The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro- inflammatory cytokines. PLoS genetics 2012;8:e1002552 2. Ylipaasto P, Kutlu B, Rasilainen S, Rasschaert J, Salmela K, Teerijoki H, Korsgren O, Lahesmaa R, Hovi T, Eizirik DL, Otonkoski T, Roivainen M: Global profiling of coxsackievirus- and cytokine-induced gene expression in human pancreatic islets. Diabetologia 2005;48:1510-1522 3. Lind K, Richardson SJ, Leete P, Morgan NG, Korsgren O, Flodstrom-Tullberg M: Induction of an antiviral state and attenuated coxsackievirus replication in type III interferon-treated primary human pancreatic islets. J Virol 2013;87:7646-7654 ABCD E ADAR ADAR ADAR ADAR ADAR BAG3 BAG3 BAG3 BAG3 BAG3 BST2 BST2 BST2 BST2 BST2 CASP1 CASP1 CASP1 CASP1 CASP1 CAV1 CAV1 CAV1 CAV1 CAV1 CCL2 CCL2 CCL2 CCL2 CCL5 CCL5 CCL5 CCL5 CD70 CD70 CD70 CD70 CD70 CD86 CD86 CD86 CD86 CDKN1B CDKN1B CDKN1B CDKN1B CIITA CIITA CIITA CDKN1B CIITA CRP CRP CRP CRP CXCL10 CXCL10 CXCL10 CXCL10 CXCL10 DDX58 DDX58 DDX58 DDX58 DDX58 EIF2AK2 EIF2AK2 EIF2AK2 EIF2AK2 EIF2AK2 GBP1 GBP1 GBP1 GBP1 GBP1 HLA-A HLA-A HLA-A HLA-A HLA-A HLA-B HLA-B HLA-B HLA-B HLA-B HLA-E HLA-E HLA-E HLA-E HLA-E IFI16 IFI16 IFI16 HLA-G IFI16 IFI27 IFI27 IFI27 IFI16 IFI27 IFI30 IFI30 IFI30 IFI27 IFI30 IFI6 IFI6 IFI6 IFI30 IFI6 IFIH1 IFIH1 IFIH1 IFI6 IFIH1 IFIT1 IFIT1 IFIT1 IFIH1 IFIT1 IFIT2 IFIT2 IFIT2 IFIT1 IFIT2 IFIT3 IFIT3 IFIT3 IFIT3 IFITM1 IFITM1 IFITM1 IFIT3 IFITM1 IFITM2 IFITM2 IFITM2 IFITM1 IFITM2 IFITM3 IFITM2 IFITM3 IFITM3 IFITM3 IFNA1 IFNA1 IFNA1 IFNA1 IFNA1 IFNA2 IFNA2 IFNA2 IFNA2 IFNA4 IFNA2 IFNA4 IFNA4 IFNA4 IFNA4 IFNAR1 IFNAR1 IFNAR1 IFNAR1 IFNAR1 IFNAR2 IFNAR2 IFNAR2 IFNAR2 IFNAR2 IFNB1 IFNB1 IFNB1 IFNB1 IFNB1 IFNE IFNE IFNE IFNE IFNW1 IFNW1 IFNW1 IFNW1 IL10 IL10 IL10 IL10 IL15 IL15 IL15 IL15 IL6 IL6 IL6 IL6 IRF1 IRF1 IRF1 IRF1 IRF1 IRF2 IRF2 IRF2 IRF2 IRF2 IRF3 IRF3 IRF3 IRF3 IRF3 IRF5 IRF5 IRF5 IRF5 IRF5 IRF7 IRF7 IRF7 IRF7 IRF7 IRF9 IRF9 IRF9 IRF9 IRF9 ISG15 ISG15 ISG15 ISG15 ISG15 ISG20 ISG20 ISG20 ISG20 ISG20 JAK1 JAK1 JAK1 JAK1 JAK2 JAK2 JAK2 JAK2 MAL MAL MAL MAL MET MAL MET MET MET MET MNDA MNDA MNDA MNDA MX1 MX1 MX1 MX1 MX2 MX1 MX2 MX2 MX2 MX2 MYD88 MYD88 MYD88 MYD88 NMI MYD88 NMI NMI NMI NMI NOS2 NOS2 NOS2 OAS1 NOS2 OAS1 OAS1 OAS1 OAS2 OAS1 OAS2 OAS2 OAS2 PML OAS2 PML PML PML PRKCZ PML PRKCZ PRKCZ PRKCZ PSME2 PRKCZ PSME2 PSME2 PSME2 PSME2 SHB SHB SHB SHB SHB SOCS1 SOCS1 SOCS1 SOCS1 STAT1 STAT1 STAT1 STAT1 STAT1 STAT2 STAT2 STAT2 STAT2 STAT2 STAT3 STAT3 STAT3 STAT3 TAP1 TAP1 TAP1 TAP1 TAP1 TICAM1 TICAM1 TICAM1 TICAM1 TIMP1 TIMP1 TIMP1 TLR3 TIMP1 TLR3 TLR3 TLR3 TLR3 TLR8 TLR8 TLR8 TLR8 TLR9 TLR9 TLR9 TLR9 TMEM173 TMEM173 TMEM173 TMEM173 TNFSF10 TNFSF10 TNFSF10 TNFSF10 TNFSF10 TRAF3 TRAF3 TRAF3 TRAF3 TRAF3 TYK2 TYK2 TYK2 TYK2 VEGFA VEGFA VEGFA VEGFA VEGFA 5 5 1 2 4 8 4 8 5 5 .5 1 2 4 8 2 4 6 5 5 1 2 4 8 4 5 5 1 2 4 8 4 25 .5 2 25 25 .2 0 16 3 6 .5 25 25 16 32 6 5 .5 1 2 4 8 4 8 25 2 0 16 32 6 56 1 .1 0 128 25 25 0 16 32 6 28 .25 0. 25 25 .25 0 16 32 6 56 62 .1250. 12 2 3 .06250 .1250.25 1 256 .1250 128 256 6 1 62 1250 12 2 5 31 06 0 .0 0 56 312.0620 56 31 .0620 0. 0 0. 01560 .0 0 .0 0 0.0 .01 0. 0. 0 0 .0150.03 0 0.01 0.01 0 ©2016 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db16-0616/-/DC1 .
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