ADAR and hnRNPC deficiency synergize in activating endogenous dsRNA-induced type I IFN responses

For RNA preparation from THP-1, cells were precipitated (350 g, 5 min, RT) and prepared using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions, including the recommended on-column DNase digest. For RNA preparation from primary monocytes/macrophages, cells were detached using Trypsin/EDTA and prepared using the Qiagen AllPrep DNA/RNA Mini Kit. RNA was either directly employed for cDNA synthesis or, to ensure proper detection of secondary-structure-rich RNA, mixed with water for cDNA synthesis, heated to 95°C for 30 s to denature secondary structures, and cooled to 4°C; then, cDNA was synthesized using the iScript cDNA synthesis kit according to the manufacturer’s instructions. cDNA was then diluted 1:20, and Taqman qPCR was performed with the following reactions per well: 5 µl TaqMan Universal PCR Master Mix, 2.5 µl water, 0.5 µl Thermo Fisher Scientific TaqMan Gene Expression Assay (FAM-MGB), and 2 µl diluted cDNA. SYBR green qPCR was performed using 5 µl SYBR Select Mastermix, 0.3 µl primer-mix (10 µM each), 2.7 µl water, and 2 µl diluted cDNA per well. qPCR was performed using a QuantStudio5 using the standard protocol (40 cycles) and relative expression using RPL36 (Fig. 1 C; and Fig. S2, A–C) or CASC3 (all other figures) as housekeeping gene was determined using the comparative cycle threshold (ΔΔCt) method. Thermo Fisher Scientific qPCR assays used in this study were CASC3: Hs00201226_m1, CXCL10: Hs00171042_m1, IFI27: Hs01086373_g1, IFIT1: Hs03027069_s1, IFIT2: Hs00533665_m1, IFNB1: Hs01077958_s1, RPL36: Hs03006033_g1, NUCKS1: Hs01068055_g1, MFSD1: Hs00224178_m1, IARS2: Hs01058378_m1, and EIF3D: Hs01044815_m1. SYBR green primers are listed in Table S4.

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