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4 protocols using α ripk1

1

Cloning and Mutagenesis of Constructs

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Constructs were generated by PCR and cloned into pAc, pMT, pcDNA3 (Invitrogen) or pEF6 and verified by sequencing. Specific point mutations were generated using site-directed mutagenesis with Pfu Turbo polymerase (Stratagene). The Ub-sgg10 fusion construct was generated by PCR using Easy-A polymerase and cloned into pMT-V5/His. The following antibodies were used: α-MYC (Sigma, M5546, 1:2,000), α-HA (Roche, 11867423001, 1:2,000), α-V5 (Serotec, MCA1360, 1:2,000), α-RIPK1 (BD Biosciences, 610459,1:1,000 for western blotting (WB) and 1:50 for immunofluorescence studies), α-Actin (Santa Cruz, sc-1615, 1:4,000), α-MYO7A (Developmental Studies Hybridoma Bank, 138-1-s, 1:1,000 for WB and 1:50 for immunofluorescence studies), α-CASP8 for WB (MBL, M032-3, 1:5,000), α-CASP8 to detect cleaved CASP8 (for human: R&D, AF1650, 1:2,000; for mouse: Cell Signaling Technology, 9429, 1:1,000), rabbit and goat α-CASP8 (Santa Cruz Biotechnology, sc-7890 and sc-6136, both 1:50 for immunofluorescence studies), CF488A-donkey α-mouse IgG (Biotium, A21202, 1:1,000), CF633-donkey α-rabbit IgG (Biotium, 20125, 1:1,000) and CF633-donkey α-goat IgG (Biotium, 20127, 1:1,000). SM (SM164) was a gift from Shaomeng Wang (University of Michigan) and TNF was obtained from Enzo Life Sciences. Uncropped WBs are shown in Supplementary Fig. 5.
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2

RIPK1 Kinase Inhibitor Mechanism Study

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The GSK’963 RIPK1 kinase inhibitor was provided by GSK. The following antibodies were used: α-RIPK1 (BD Biosciences, 610459), α-HOIL (gift from Henning Walczak), α-cIAP1 (Enzo, ALX-803-335-C100), α-TNFR1 (Abcam, 19139), α-Actin (Santa Cruz Biotechnology, sc-1615), α-P-p65 (Cell Signaling, 3033), α-p65 (Cell Signaling, 8242), α-IkBα (Santa Cruz, sc-371), α-P-p38 (Cell Signaling, 9215), α-p38 (Cell Signaling, 9212), α-P-JNK (Cell Signaling, 9255), α-JNK (Santa Cruz Biotechnology, sc-571), α-P-ERK (Cell Signaling, 9101), α-ERK (gift from Chris Marshall) α-caspase-8 (Cell Signaling, 9429), α-FLAG [M2] (SIGMA, M8823), α-Ub (Dako, Z0458), α-FLIP (Adipogene, AG-20B-0056), α-FADD (Santa Cruz Biotechnology, sc-6036), α-RIPK3 (ProSci, 2283), α-Tubulin (SIGMA, T9026), α-SHARPIN (Proteintech, 14626-1-AP), α-TRAF2 (Cell Signaling, 4712), α-CD8-PE-Cy7, GR-1-PE-Cy7, CD11c-FITC, CD4-FITC, CD11b-Cy5, B220-FITC (gift from Henning Walczak), α-CD69-PE (eBioscience, 12-0691-82), α-CD3-APC (eBioscience, 47-0032-82), and α-CD16 (eBioscience, 14-0161-82).
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3

Immunoprecipitation of RIPK1 and ZBP1 from BMDMs

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Indicated BMDMs were plated on 6-well tissue-culture-treated plates, stimulated as indicated, and harvested in immunoprecipitation lysis buffer (0.5% Triton X, 50 mM Tris Base [pH 7.4], 150 mM NaCl, 2 mM ethylenediaminetetraacetic acid, 2 mM ethylene glycol tetraacetic acid, 1X protease inhibitor mixture). Lysed cells were rotated for 60 min at 4 °C with intermittent vortexin and centrifuged at 5,000 X g for 5 min, and the supernatant was incubated with α-RIPK1 (BD Biosciences 610459) or α-ZBP1 (AG-20B-0010-C100) antibody-conjugated protein G agarose beads (Cell Signaling Technology 37478). Samples were washed three times in immunoprecipitation lysis buffer, and protein complexes were eluted with 1X Laemmli buffer containing 5% β-mercaptoethanol at 90 °C for 15 min.
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4

Investigating Cell Death Pathways

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The following reagents were used: zVAD-FMK (10 μM, Apex Bio), QVD (10 μM, Apex Bio), SM-164 (100 nM, gift from Shaomeng Wang), GSK’963 (referred as RIPK1i, 100 nM, GlaxoSmithKline), Nec-1 (10 μM Merck), Nec-1s (10 μM Merck), RO-3306 (9 μM, Merck), Thymidine (Sigma), BIM peptide (Kind gift of Tony Letai), FLAG-hTNF (10 ng/ml, Enzo), MG132 (1-20 μM, as indicated per cell line, see below, SIGMA), Recombinant Casp8 (1U Enzo). The following antibodies were used for western blotting: α-RIPK1 (1:1000, BD Biosciences), α-HA (1:1000, Roche), α-PLK1 (1:1000, Bethyl Laboratories), α-PLK1-pT210 (1:2000, AbCam), α-Cyclin B (1:1000, Cell Signaling), α-BUBR1 (1:1000, BD Bioscience), α-BUBR1-pT680 (1:1000, Kind gift of Geert J.P.L Kops), α-BUBR1-pT676 (1:1000, Kind gift of Erich A. Nigg), α-pH-H3 (1:2000, Millipore), α-Casp8 (for WB - post IP, 1:5000, MBL), α-Casp8 - for IP (7.5 μg/ml, C-20, Santa Cruz Biotechnology, α-FADD – for IP (7.5 μg/ml, Santa Cruz), α-FADD (1:1000 BD Biosciences), α-RIPK3 (1:1000 Proscience), α-RIPK3 (1:1000 Novus Biological) α-cFLIP (1:1000, Enzo), α-Myc (1:1000, clone 9E10,SIGMA), α-HSP90 (1:1000 Santa Cruz Biotechnology).
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