REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Antibodies | ||
Anti-ERK1 + ERK2 antibody | Abcam | Cat# ab17942 |
anti-β-actin | Santa Cruz Biotechnology | Cat# I-19 |
anti-RIPK1 | BD-Biosciences | Cat# 610459 |
anti-β-tubulin | Abcam | Cat# ab6046 |
anti-β-tubulin-HRP | Abcam | Cat# ab21058 |
Anti-MAP Kinase, Activated (Diphosphorylated ERK-1&2) antibody | Sigma Aldrich | Clone MAPK-YT, M9692 |
anti-MLKL | Merck Millipore | Cat# MABC604, Clone 3H1 |
Anti-phospho-MLKL (Ser345) | Merck Millipore | Cat# MABC1158, clone 7C6.1 |
Phospho-MEK1/2 (Ser217/221) | Cell Signalling | Cat# 9121 |
Anti-MEK1/2 | Cell Signalling | Cat# 9122 |
anti-RIPK3 | Santa Cruz | Cat# sc-374639 |
anti-RSK1/2/3 | Cell Signalling | Cat# 9355, clone 32D7 |
anti-phspho-p90-RSK (Ser380) | Cell Signalling | Cat# 9341 |
anti-GSK3β | Cell Signalling | Cat# 12456, clone D5C5Z-XP |
anti-phospho-GSK-3α/β | Cell Signalling | Cat# 9331 |
anti-mouse Alexa Fluor 488 | Thermo Fischer | Cat# A-10667 |
HRP-conjugated anti-rabbit IgG | Santa Cruz Biotechnology | Cat# sc-2004 |
HRP-conjugated anti-mouse IgG | Santa Cruz Biotechnology | Cat# sc-2005 |
HRP-conjugated anti-goat IgG | Santa Cruz Biotechnology | Cat# sc-2020 |
HRP-conjugated anti-rat- IgG | GE Healthcare | Cat# NA935 |
Chemicals, peptides, and recombinant proteins | ||
Recombinant mouse TNFα | In house production | N/A |
Anti-hFas ligand | Upstate | Cat# 05-201Clone CH11 |
Phorbol 12-myristate 13-acetate (PMA) | Sigma Aldrich | Cat# P8139 |
U0126 | Sigma Aldrich | Cat# U120 |
PD184352 | Sigma Aldrich | Cat# PZ0181 |
AZ628 | Sigma Aldrich | Cat# SML0785 |
BI-D1878 | Sigma Aldrich | Cat# 559286 |
Forskoline | Tocris | Cat# 1099/10 |
SCH772984 | Selleckchem | Cat# S7101 |
Selumetinib (AZD6244) | Selleckchem | Cat# S1008 |
Trametinib (GSK1120212) | Selleckchem | Cat# S2673 |
Necrostatin-1S (Nec1S) | Laboratory of Medicinal Chemistry; University of Antwerp | Cat# UAMC-02197 |
Propidium Iodide | Sigma Aldrich | Cat# P-4170 |
Sytox Green | Thermo Fischer Scientific | Cat# S7020 |
Doxycycline Hyclate (Dox) | Sigma Aldrich | Cat# D9891 |
Rneasy Mini Kit | Qiagen | Cat# 74104 |
Qiashredder | Qiagen | Cat# 79654 |
DNA-free™ DNA Removal Kit | Invitrogen | Cat# AM1906 |
SuperScript® III First-Strand Synthesis System for RT-PCR | Invitrogen | Cat# 18080-51 |
qPCR MasterMix Plus for SYBR® Green I No ROX | Eurogentec | Cat# RT-SN2X-03+NR |
Ac-DEVD-AMC | Pepta Nova | Cat# 3171-V |
Bio-Gel P-6 Micro Bio-Spin chromatography columns | Biorad | Cat# 732-6222 |
plasmid purification columns | Qiagen | Cat# 28106, 28706, and 27106 |
PCR colony screening kit | 5Prime | Cat# MasterTaq Kit |
Q5 DNA polymerase | NEB | Cat# M0491 |
Taq DNA polymerase | NEB | Cat# M0273 |
Klenow fragment | NEB | Cat# M0212 |
T4 Polynucleotide Kinase (PNK) | NEB | Cat# M0201 |
T4 DNA ligase | NEB | Cat# M0202 |
dNTPs | NEB | Cat# N0447 |
ATP | NEB | Cat# P0756 |
Restriction Enzymes, endonucleases | NEB | N/A |
four-fragment Multisite Gateway Pro Plus system | Life Technologies | Cat# 12537-100 |
EDTA-free Complete protease inhibitor cocktail tablets | Roche Diagnostics Belgium | Cat# 11873580001 |
phosphatase inhibitor cocktail tablets | Roche Diagnostics Belgium | Cat# 04906837001, PhosSTOP |
Luminata Classico Western HRP Chemiluminescence Detection Reagents | Millipore | Cat# WBLUC0500 |
Experimental models: Cell lines | ||
HeLa | ECACC | Cat# 93021013 |
HEK 293T | ATCC | Cat# CRL-11268 |
L929sAhFas | Generated in our unit | N/A |
HT-29 | ATCC | Cat# ATCC-HTB-38 |
inducible mRIPK3-CT26 | Generated in our unit | Aaes et al. (2016) |
Fadd-/-Jurkat | Generated in our unit | N/A |
Mlkl-/- L929sAhFas | Generated in our unit | N/A |
inducible mMLKL(S345D)-L929sAhFas | Generated in our unit | N/A |
Recombinant DNA | ||
AKAR4.0 | This study | N/A |
EKAR4.0 | This study | N/A |
AKAR3-EV | Kindly provided by the Michiyuki Matsuda laboratory (Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Kyoto, Japan) | Komatsu, N., Aoki, K., Yamada, M., Yukinaga, H., Fujita, Y., Kamioka, Y., and Matsuda, M. (2011). Development of an optimized backbone of FRET biosensors for kinases and GTPases. Mol. Biol. Cell 22, 4647–4656. |
AKAR-EV (T>A) | This study | N/A |
EKAR-EV | Kindly provided by the Michiyuki Matsuda laboratory (Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Kyoto, Japan) | Komatsu, N., Aoki, K., Yamada, M., Yukinaga, H., Fujita, Y., Kamioka, Y., and Matsuda, M. (2011). Development of an optimized backbone of FRET biosensors for kinases and GTPases. Mol. Biol. Cell 22, 4647–4656. |
EKAR-EV (T>A) | This study | N/A |
EKAR2G-WT | A gift from Olivier Pertz | Addgene plasmid # 39813 ; http://n2t.net/addgene:39813 ; RRID:Addgene_39813 |
EKAR2G-105/WT | A gift from Olivier Pertz | Addgene plasmid # 39818 ; http://n2t.net/addgene:39818 ; RRID:Addgene_39818 |
EKAR-EV-VV | Previously developed | Vandame, P., Spriet, C., Riquet, F., Trinel, D., Cailliau-Maggio, K., and Bodart, J.-F. (2014). Optimization of ERK activity biosensors for both ratiometric and lifetime FRET measurements. Sensors (Basel). 14, 1140–1154. |
pDG2-flag-rtTA3-puro-mRIPK3 | Previously generated in our unit | Aaes et al. (2016) |
pDG2-flag-rtTA3-puro-mMLKL(S345D) | Generated in our unit | N/A |
Software and algorithms | ||
Statistical analyses | GraphPad Prism | PRISM 8 software, RRID: SCR_002798 |
qPCR analysis | Biogazelle | qBasePLUS, RRID: SCR_003370 |
FRET analysis (short experiment) | IGOR Pro - Wavemetrics | Ratioscope_8.31, DOI:10.25493/5G5V-HBC |
FRET analysis (long experiment) | Matlab, MathWorks | CellTraFIC code, RRID: SCR_001622 |
CellTraFIC (Cellular Tracking in FRET Image aCquisition) | APP Paris | IDDN.FR.001.230009.000.S.P. 2017.000.21000 |
CellTraFIC (Cellular Tracking in FRET Image aCquisition) | GitHub | https://github.com/ayleray/CellTraFIC |
Cell Death Analysis | Fiji | RRID: SCR_002285 |
Immunofluorescence quantification | Cell Profiler | RRID: SCR_007358 |