Virus:Article Title: ArreSTick motif controls β-arrestin-binding stability and extends phosphorylation-dependent β-arrestin interactions to non-receptor proteins.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit anti-b-arrestin2 Cell Signaling Technology Cat#3857S; RRID: AB_2258681 rabbit anti-b-arrestin1 Cell Signaling Technology Cat#30036S; RRID: AB_2798985 HRP-conjugated anti-rabbit Cell Signaling Technology Cat#7074S; RRID: AB_2099233 HRP-conjugated anti-mouse Cell Signaling Technology Cat#7076S; RRID: AB_330924 anti-HTATSF1 Proteintech Cat#20805-I-AP; RRID: AB_10695767 Alexa 488-conjugated secondary goat anti-rabbit antibody Invitrogen Cat#A11034; RRID: AB_2576217 Bacterial and virus strains Supercompetent cells home-made N/A Chemicals, peptides, and recombinant proteins Biotin SERVA Electrophoresis GmbH Cat#15060.03 High Capacity NeutrAvidin-Agarose Resin Thermo Scientific Cat#29204 GFP-Trap Magnetic Agarose resin Chromotek Cat#gtma-20 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat#P1585-5MG Poly-L-lysine Sigma-Aldrich Cat#P8920-100ML Lipofectamine 2000 Invitrogen Cat#52887 DMEM VWR Cat#392-0416 Penicillin/Streptomycin Lonza Cat#DE17-602E Fetal bovine serum Biosera Cat#FB-1090/500 SDS SERVA Cat#20760.03 Plasmocin InvivoGen Cat#MPP-44-02 Coelenterazine h Regis Technologies Cat#1-361304-200 Arginine vasopressin Sigma-Aldrich Cat#V9879-1MG Angiotensin II Sigma-Aldrich Cat#A9525-5x1MG A61603 Tocris Cat#1052 DAPI Sigma-Aldrich Cat#A2547-2ML cOmplete Protease Inhibitor Roche Cat#11836145001 Phosphatase Inhibitor Mixture 3 Sigma-Aldrich Cat#P0044-1ML Sodium deoxycholate (SOC) Sigma-Aldrich Cat#D6750-25G Sodium pyrophosphate Sigma-Aldrich Cat#S-6422 Sodium orthovanadate Sigma-Aldrich Cat#S6508-10G Sodium fluoride Sigma-Aldrich Cat#S7920-100G b-Glycerophosphate Sigma-Aldrich Cat#G9422-100G Triton X-100 Sigma-Aldrich Cat#T8787-100ML Iodoacetamide (IAA) Fluka Chemie GmbH Cat#57670 1,4-Dithiothreitol (DTT) Roche Diagnostics Cat#10 197 777 001 Trypsin Gold, Mass Spectrometry Grade Promega Cat#V5280 Disuccinimidyl suberate (DSS) PIERCE Cat#21555 Immobilon Western chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 Bovine Serum Albumin (BSA) Sigma-Aldrich Cat#A3059-100G Methanol MOLAR Chemical Cat#05730-101-340 Ethanol MOLAR Chemical Cat#02910-101-340 Paraformaldehyde Polysciences Cat#18814-20 (Continued on next page) Cell Reports 43, 114241, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER SOC Invitrogen Cat#15544-034 RapiGest Waters Cat#186001860 Deposited data Western blot original images Mendeley Mendeley Data: https://doi.org/10.17632/j7xhxfzdsx.1 Mass spectrometry data MassIVE MassIVE Data: ftp://massive.ucsd.edu/v06/MSV000092868/ Experimental models: Cell lines HEK 293T ATCC Cat#CRL-3216 HEK 293A parent O’Hayre et al.25 N/A HEK 293A barr1/2-KO O’Hayre et al.25 N/A Recombinant DNA pEYFP-N1 wt-barr2–Venus Gyombolai et al.5 N/A pEYFP-N1 K2A-barr2–Venus Tóth et al.20 N/A pEYFP-N1 wt-barr2–Rluc8 Turu et al.67 N/A pEYFP-N1 K2A-barr2–Rluc8 This paper N/A pEYFP-N1 wt-barr1–Venus Gyombolai et al.5 N/A pEYFP-N1 K2A-barr1–Venus This paper N/A pEYFP-N1 wt-barr1–Rluc8 This paper N/A pEYFP-N1 K2A-barr1–Rluc8 This paper N/A pEGFP-N1 L10–mRFP This paper N/A pEGFP-N1 AT1R-Cterm–Venus This paper N/A pEGFP-N1 AT1R-Cterm-TSTS/A–Venus This paper N/A pEGFP-N1 V2R-Cterm–Venus This paper N/A pEYFP-N1 wt-barr2–TurboID This paper N/A pEYFP-N1 K2A-barr2–TurboID This paper N/A pcDNA3.1+ adrenergic receptor alpha 1A cDNA Resource Center Cat##AR0A1A0001 pCMV6 HTATSF1 Origene Cat#SC114990 pEYFP-N1 GRK5–FLAG This paper N/A pCMV5 barr1 (rat) Dr. Stephen S. G. Ferguson N/A pCMV5 barr2 (rat) Dr. Stephen S. G. Ferguson N/A pEYFP-N1 HTSF1–mNeonGreen This paper N/A pEYFP-N1 HTSF1-ST/AA–mNeonGreen This paper N/A pEYFP-N1 HTSF1–Venus This paper N/A pEYFP-N1 HTSF1-ST/AA–Venus This paper N/A Software and algorithms Byonic https://proteinmetrics.com/byonic/ v3.5.0, Protein Metrics Inc GraphPad Prism 9 https://www.graphpad.com GraphPad Prizm Software MaxQuant https://www.maxquant.org/ software version 1.6.7 Compass Data Analysis software 4.3 Bruker Daltonik GmbH Version 4.3 Python code This paper Zenodo: https://doi.org/10.5281/zenodo.10804718 Cell analysis python code This paper Zenodo: https://doi.org/10.5281/zenodo.10072720 Other 96-well white flat bottom plates Greiner Cat#655083 10 cm cell culture dish Greiner Cat#664160 m-Slide 8 Well Ibidi plate Ibidi GmbH Cat#80826 PVDF transfer membrane Thermo Scientific Cat#88518 18 Cell Reports 43, 114241, May 28, 2024
Article Title: Cytoplasmic calcium influx mediated by plant MLKLs confers TNL-triggered immunity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat Monoclonal Anti-HA Sigma-Aldrich Cat# 11867423001 Goat Anti-Rat Sigma-Aldrich Cat# AP136P Rabbit Polyclonal Anti-GFP Abcam Cat# ab6556 Goat Anti-Rabbit Sigma-Aldrich Cat# A9169 Mouse Monoclonal Anti-FLAG Sigma-Aldrich Cat# F1804 Goat Anti-Mouse Sigma-Aldrich Cat# A9316 Horseradish peroxidase (HRP)-coupled Anti-DYKDDDDK Miltenyi Biotec Cat# 130-101-572 Horseradish peroxidase (HRP)-coupled Anti-HA Miltenyi Biotec Cat# 130-091-972 Mouse monoclonal Anti- Alpha-Tubulin Sigma-Aldrich Cat# T6074 HRP-coupled Anti-mouse Cell Signaling Technology Cat# 7076S Bacterial and virus strains Chemically Competent E. coli MPIPZ stock N/A Electrically Competent A. tumefaciens GV3101 (pMP90RK or pMP90Rgent) MPIPZ stock N/A Pseudomonas syringae pv. tomato (Pst) DC3000 Mahdi et al.10 N/A Xanthomonas campestris pv vesicatoria (Xcv 85-10) Thieme et al.87 N/A P. fluorescens 0-1 expressing empty vector (Pf0-EV) Saucet et al.42 N/A P. fluorescens 0-1 expressing AvrRps4 (Pf0-AvrRps4) Saucet et al.42 N/A P. fluorescens 0-1 expressing AvrRpm1(Pf0-AvrRpm1) Grant et al.56 N/A P. fluorescens 0-1 expressing XopQ (Pf0-XopQ) Schultink et al.43 N/A Biological samples Arabidopsis thaliana leaves Arabidopsis thaliana N/A Arabidopsis thaliana protoplasts Arabidopsis thaliana N/A Nicotiana benthamiana leaves Nicotiana benthamiana N/A Chemicals, peptides, and recombinant proteins Brefeldin A Sigma-Aldrich Cat# B6542 Cycloheximide Sigma-Aldrich Cat# 239763-M Chitin (NA-COS-Y) Mahdi et al.10 N/A Flagellin epitope flg22 MPIPZ stock N/A Oryzalin Sigma-Aldrich Cat# 36182 Fluo-4 AM AAT Bioquest Cat# 20551 FM4-64 Sigma-Aldrich Cat# SCT127 Critical commercial assays RNeasy Plant Mini Kit QIAGEN Cat# 74904 4x Laemmli Sample Buffer Bio-Rad Cat# 1610747 GFP Selector magnetic beads NanoTag Cat# N0310 Experimental models: Cell lines Sf21 insect cells Invitrogen Cat# 11497013 Human embryonic kidney, HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Arabidopsis: Col-0 MPIPZ stock N/A Arabidopsis: mlkl123 Mahdi et al.10 N/A Arabidopsis: MLKL1-GFP Mahdi et al.10 N/A Arabidopsis: eds1-12 Ordon et al.53 N/A (Continued on next page) e1 Cell Host & Microbe 32, 453–465.e1–e6, April 10, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Arabidopsis: MLKL1-GFP in eds1-12 This paper N/A Arabidopsis: 35S::Helo-GFP in mlkl123 This paper N/A Arabidopsis: 35S::GCaMP3 in Col-0 Vincent et al.55 N/A Arabidopsis: 35S::GCaMP3 in mlkl123 This paper N/A Arabidopsis: 35S::GCaMP3 in nrg1.1,1.2 This paper N/A Nicotiana: WT This paper N/A Nicotiana: eds1a, pad4, sag101a, sag101b Lapin et al.24 N/A Nicotiana: 35S::GCaMP3 in WT DeFalco et al.57 N/A Oligonucleotides See Table S1 for primers This paper N/A Recombinant DNA pUC19-AvrRps4-3xFLAG Xing et al.88 N/A pAMPAT-35S-mClover3 This paper N/A pAMPAT-35S-HeLo-mClover3 This paper N/A pAMPAT-35S-HeLoBrace-mClover3 This paper N/A pAMPAT-35S-HeLoBracePseudokinase-mClover3 This paper N/A pAMPAT-35S-AtMLKL1-mClover3 This paper N/A pAMPAT-35S-BracePseudokinaseID-mClover3 This paper N/A pAMPAT-35S-HeLo-3xHA This paper N/A pAMPAT-35S-HeLoBrace-3xHA This paper N/A pAMPAT-35S-HeLoBracePseudokinase-3xHA This paper N/A pAMPAT-35S-AtMLKL1-3xHA This paper N/A pAMPAT-35S-BracePseudokinaseID-3xHA This paper N/A pXCSG-35S-HB-3xHA This paper N/A pXCSG-35S-HP-3xHA This paper N/A pXCSG-35S-HH-3xHA This paper N/A pXCSG-35S-HH+HP-3xHA This paper N/A pXCSG-35S-HP+HB-3xHA This paper N/A pXCSG-35S-S393D-3xHA This paper N/A pSfinx-mYFP This paper N/A pAMPAT-35S-AtMLKL1-cYFP This paper N/A pESPY-35S-AtSAG101-nYFP This paper N/A pXCSG-AtEDS1-FLAG Lapin et al.24 N/A pXCSG-AtSAG101-FLAG Lapin et al.24 N/A pXCSG-AtNRG1.1-3xHA Lapin et al.24 N/A pXCSG-GUS-FLAG Lapin et al.24 N/A pBIN20-35S-GCaMP3 Vincent et al.55 N/A pMDC7-HeLo-3xHA This paper N/A pGWB517-35S-P19 This paper N/A pGWB517-35S-CMV2b This paper N/A pcDNA 5/FRT/TO- HsMLKL (HeLo+Brace)-FLAG This paper N/A pcDNA 5/FRT/TO- AtMLKL (HeLo)-FLAG This paper N/A pcDNA 5/FRT/TO- AtMLKL (HeLo+Brace)-FLAG This paper N/A Software and algorithms Fiji Schindelin et al.89 https://fiji.sc/ R studio RStudioTeam, 2018 http://www.rstudio.com/ Alfafold2 Jumper et al.49 https://alphafold.com/ Cell Host & Microbe 32, 453–465.e1–e6, April 10, 2024 e2
Article Title: Microglial lipid phosphatase SHIP1 limits complement-mediated synaptic pruning in the healthy developing hippocampus.
Article Snippet: In brief Inpp5d, which encodes the lipid phosphatase SHIP1, is a risk gene for Alzheimer’s disease, but its role in brain development has been poorly studied.. Matera, Compagnion et al. demonstrate that Inpp5d is expressed in microglia during early postnatal brain development, where it limits synaptic pruning in a complement-dependent manner, and that its perturbation during brain development has long-lasting effects on cognitive function.
Article Title: Nuclear and cytosolic fractions of SOX2 synergize as transcriptional and translational co-regulators of cell fate.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal (D6D9) anti-SOX2 Cell Signaling Technology Cat#3579; RRID:AB_2195767 Rabbit monoclonal (D8G8H) anti-SOX9 Cell Signaling Technology Cat#82630; RRID:AB_2665492 Rabbit polyclonal anti-OCT4 (aka POU5F1) Cell Signaling Technology Cat#2750; RRID:AB_823583 Rabbit polyclonal anti-KLF4 Cell Signaling Technology Cat#4038; RRID:AB_2265207 Rabbit monoclonal (D84C12) anti-cMYC Cell Signaling Technology Cat#5605; RRID:AB_1903938 Rabbit monoclonal (5G10) anti-RPS6 Cell Signaling Technology Cat#2217; RRID:AB_331355 Rabbit monoclonal (2F9) anti-pRPS6 (Ser235/236) Cell Signaling Technology Cat#4856; RRID:AB_2181037 Rabbit monoclonal (D68F8) anti-pRPS6 (Ser240/244) Cell Signaling Technology Cat#5364; RRID:AB_10694233 Rabbit monoclonal (C67E7) anti-panAKT Cell Signaling Technology Cat#4691; RRID:AB_915783 Rabbit monoclonal (D9E) anti-pAKT (Ser473) Cell Signaling Technology Cat#4060; RRID:AB_2315049 Rabbit monoclonal (108E2) anti-pS6K1 (Thr389) Cell Signaling Technology Cat#9234; RRID:AB_2269803 Rabbit monoclonal (D4B8) anti-ATF4 Cell Signaling Technology Cat#11815; RRID:AB_2616025 Rabbit monoclonal (D64F1) anti-CHOP Cell Signaling Technology Cat#5554; RRID:AB_10694399 Rabbit polyclonal anti-eIF2alpha Cell Signaling Technology Cat#9722; RRID:AB_2230924 Rabbit monoclonal (119A11) anti-peIF2alpha (Ser51) Cell Signaling Technology Cat#3597; RRID:AB_390740 Rabbit monoclonal (12D1) anti-p21 (aka Waf1/Cip1) Cell Signaling Technology Cat#2947; RRID:AB_823586 Rabbit monoclonal (D1H1) anti-H3 Cell Signaling Technology Cat#4499; RRID:AB_10544537 Rabbit monoclonal (D16H11) anti-GAPDH Cell Signaling Technology Cat#5174 Rabbit monoclonal (8H10D10) anti-beta-actin Cell Signaling Technology Cat#3700; RRID:AB_10622025 Rabbit monoclonal (9F3) anti-beta-tubulin Cell Signaling Technology Cat#2128; RRID:AB_823664 Rabbit polyclonal anti-RPL3 Abcam ab154882 Rabbit polyclonal anti-RPL23 Sigma-Aldrich HPA003373; RRID:AB_1856436 Mouse monoclonal anti-mCherry Clontech, TakaRa Bio Living Colors #632543; RRID:AB_2307319 Mouse monoclonal (9E10) anti-cMyc Invitrogen #13-2500; RRID:AB_2533008 HRP-linked anti-rabbit Cell Signaling Technology Cat#7074; RRID:AB_2099233 (Continued on next page) Cell Reports 43, 114807, October 22, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER HRP-linked anti-mouse Cell Signaling Technology Cat7076; RRID:AB_330924 Streptavidin-HRP conjugate R&D Systems #890803 isotype control (official product name: ‘‘Normal’’ rabbit IgG) Santa Cruz Biotechnology sc-3888; RRID:AB_145841 Bacterial and virus strains OneShotTM chemically competent TOP10 E.coli Thermo-Fisher C404003 Biological samples No primary biological samples were used in this study. .. Chemicals, peptides, and recombinant proteins Cycloheximide Sigma C7698 Puromycin Applichem A2856 Geneticin Gibco #11-811-031 O-propargyl-puromycin (OPP) Thermo-Fisher Click-iT Plus OPP, C10456 Oligomycin Sigma #75351 2-Deoxy-D-glucose Sigma D3179 2-Nitrobenzyl-desoxyglucose (2-NBDG) Thermo-Fisher N13195 Carbonyl-cyanide-4-(trifluoromethoxy)phenylhydrazone (FCCP) Sigma C2920 Rotenone Sigma R8875 Biotin Sigma B4639 Heparin Ratiopharm #06884371 Insulin Lonza CC-4021G Hydrocortisone Lonza CC-4031G Epidermal growth factor (EGF) Sigma E9644 Fibroblast growth factor (FGF) PeproTech #100-18B Recombinant human SOX2 Novus Biologicals NBP2-35268 Critical commercial assays FluoroTect GreenLys in vitro Translation Labeling System Promega #L5001 Click-iTTM Plus OPP Alexa FluorTM 488 Protein Synthesis Assay Kit Thermo-Fisher C10456 SMARTer smRNA-Seq Kit for Illumina Clontech, Takara Bio #635031 TruSeq Stranded Total RNA Kit V2.0 Illumina #20020594 Deposited data RNAseq raw sequencing data This paper ArrayExpress (https://www.ebi.ac.uk/ biostudies/arrayexpress) Record number: E-MTAB-13098 RIBOseq raw sequencing data This paper ArrayExpress (https://www.ebi.ac.uk/ biostudies/arrayexpress) Record number: E-MTAB-13099 RNAseq and RIBOseq analysis scripts This paper Zenodo (https://zenodo.org/) https://doi.org/10.5281/zenodo.13752731 MS hit lists This paper PRIDE (https://www.ebi.ac.uk./pride/, Dataset identifier: PXD015157 and https://doi.org/10.6019/PXD015157. (Continued on next page) 22 Cell Reports 43, 114807, October 22, 2024
Recombinant:Article Title: ArreSTick motif controls β-arrestin-binding stability and extends phosphorylation-dependent β-arrestin interactions to non-receptor proteins.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit anti-b-arrestin2 Cell Signaling Technology Cat#3857S; RRID: AB_2258681 rabbit anti-b-arrestin1 Cell Signaling Technology Cat#30036S; RRID: AB_2798985 HRP-conjugated anti-rabbit Cell Signaling Technology Cat#7074S; RRID: AB_2099233 HRP-conjugated anti-mouse Cell Signaling Technology Cat#7076S; RRID: AB_330924 anti-HTATSF1 Proteintech Cat#20805-I-AP; RRID: AB_10695767 Alexa 488-conjugated secondary goat anti-rabbit antibody Invitrogen Cat#A11034; RRID: AB_2576217 Bacterial and virus strains Supercompetent cells home-made N/A Chemicals, peptides, and recombinant proteins Biotin SERVA Electrophoresis GmbH Cat#15060.03 High Capacity NeutrAvidin-Agarose Resin Thermo Scientific Cat#29204 GFP-Trap Magnetic Agarose resin Chromotek Cat#gtma-20 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat#P1585-5MG Poly-L-lysine Sigma-Aldrich Cat#P8920-100ML Lipofectamine 2000 Invitrogen Cat#52887 DMEM VWR Cat#392-0416 Penicillin/Streptomycin Lonza Cat#DE17-602E Fetal bovine serum Biosera Cat#FB-1090/500 SDS SERVA Cat#20760.03 Plasmocin InvivoGen Cat#MPP-44-02 Coelenterazine h Regis Technologies Cat#1-361304-200 Arginine vasopressin Sigma-Aldrich Cat#V9879-1MG Angiotensin II Sigma-Aldrich Cat#A9525-5x1MG A61603 Tocris Cat#1052 DAPI Sigma-Aldrich Cat#A2547-2ML cOmplete Protease Inhibitor Roche Cat#11836145001 Phosphatase Inhibitor Mixture 3 Sigma-Aldrich Cat#P0044-1ML Sodium deoxycholate (SOC) Sigma-Aldrich Cat#D6750-25G Sodium pyrophosphate Sigma-Aldrich Cat#S-6422 Sodium orthovanadate Sigma-Aldrich Cat#S6508-10G Sodium fluoride Sigma-Aldrich Cat#S7920-100G b-Glycerophosphate Sigma-Aldrich Cat#G9422-100G Triton X-100 Sigma-Aldrich Cat#T8787-100ML Iodoacetamide (IAA) Fluka Chemie GmbH Cat#57670 1,4-Dithiothreitol (DTT) Roche Diagnostics Cat#10 197 777 001 Trypsin Gold, Mass Spectrometry Grade Promega Cat#V5280 Disuccinimidyl suberate (DSS) PIERCE Cat#21555 Immobilon Western chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 Bovine Serum Albumin (BSA) Sigma-Aldrich Cat#A3059-100G Methanol MOLAR Chemical Cat#05730-101-340 Ethanol MOLAR Chemical Cat#02910-101-340 Paraformaldehyde Polysciences Cat#18814-20 (Continued on next page) Cell Reports 43, 114241, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER SOC Invitrogen Cat#15544-034 RapiGest Waters Cat#186001860 Deposited data Western blot original images Mendeley Mendeley Data: https://doi.org/10.17632/j7xhxfzdsx.1 Mass spectrometry data MassIVE MassIVE Data: ftp://massive.ucsd.edu/v06/MSV000092868/ Experimental models: Cell lines HEK 293T ATCC Cat#CRL-3216 HEK 293A parent O’Hayre et al.25 N/A HEK 293A barr1/2-KO O’Hayre et al.25 N/A Recombinant DNA pEYFP-N1 wt-barr2–Venus Gyombolai et al.5 N/A pEYFP-N1 K2A-barr2–Venus Tóth et al.20 N/A pEYFP-N1 wt-barr2–Rluc8 Turu et al.67 N/A pEYFP-N1 K2A-barr2–Rluc8 This paper N/A pEYFP-N1 wt-barr1–Venus Gyombolai et al.5 N/A pEYFP-N1 K2A-barr1–Venus This paper N/A pEYFP-N1 wt-barr1–Rluc8 This paper N/A pEYFP-N1 K2A-barr1–Rluc8 This paper N/A pEGFP-N1 L10–mRFP This paper N/A pEGFP-N1 AT1R-Cterm–Venus This paper N/A pEGFP-N1 AT1R-Cterm-TSTS/A–Venus This paper N/A pEGFP-N1 V2R-Cterm–Venus This paper N/A pEYFP-N1 wt-barr2–TurboID This paper N/A pEYFP-N1 K2A-barr2–TurboID This paper N/A pcDNA3.1+ adrenergic receptor alpha 1A cDNA Resource Center Cat##AR0A1A0001 pCMV6 HTATSF1 Origene Cat#SC114990 pEYFP-N1 GRK5–FLAG This paper N/A pCMV5 barr1 (rat) Dr. Stephen S. G. Ferguson N/A pCMV5 barr2 (rat) Dr. Stephen S. G. Ferguson N/A pEYFP-N1 HTSF1–mNeonGreen This paper N/A pEYFP-N1 HTSF1-ST/AA–mNeonGreen This paper N/A pEYFP-N1 HTSF1–Venus This paper N/A pEYFP-N1 HTSF1-ST/AA–Venus This paper N/A Software and algorithms Byonic https://proteinmetrics.com/byonic/ v3.5.0, Protein Metrics Inc GraphPad Prism 9 https://www.graphpad.com GraphPad Prizm Software MaxQuant https://www.maxquant.org/ software version 1.6.7 Compass Data Analysis software 4.3 Bruker Daltonik GmbH Version 4.3 Python code This paper Zenodo: https://doi.org/10.5281/zenodo.10804718 Cell analysis python code This paper Zenodo: https://doi.org/10.5281/zenodo.10072720 Other 96-well white flat bottom plates Greiner Cat#655083 10 cm cell culture dish Greiner Cat#664160 m-Slide 8 Well Ibidi plate Ibidi GmbH Cat#80826 PVDF transfer membrane Thermo Scientific Cat#88518 18 Cell Reports 43, 114241, May 28, 2024
Article Title: Cytoplasmic calcium influx mediated by plant MLKLs confers TNL-triggered immunity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat Monoclonal Anti-HA Sigma-Aldrich Cat# 11867423001 Goat Anti-Rat Sigma-Aldrich Cat# AP136P Rabbit Polyclonal Anti-GFP Abcam Cat# ab6556 Goat Anti-Rabbit Sigma-Aldrich Cat# A9169 Mouse Monoclonal Anti-FLAG Sigma-Aldrich Cat# F1804 Goat Anti-Mouse Sigma-Aldrich Cat# A9316 Horseradish peroxidase (HRP)-coupled Anti-DYKDDDDK Miltenyi Biotec Cat# 130-101-572 Horseradish peroxidase (HRP)-coupled Anti-HA Miltenyi Biotec Cat# 130-091-972 Mouse monoclonal Anti- Alpha-Tubulin Sigma-Aldrich Cat# T6074 HRP-coupled Anti-mouse Cell Signaling Technology Cat# 7076S Bacterial and virus strains Chemically Competent E. coli MPIPZ stock N/A Electrically Competent A. tumefaciens GV3101 (pMP90RK or pMP90Rgent) MPIPZ stock N/A Pseudomonas syringae pv. tomato (Pst) DC3000 Mahdi et al.10 N/A Xanthomonas campestris pv vesicatoria (Xcv 85-10) Thieme et al.87 N/A P. fluorescens 0-1 expressing empty vector (Pf0-EV) Saucet et al.42 N/A P. fluorescens 0-1 expressing AvrRps4 (Pf0-AvrRps4) Saucet et al.42 N/A P. fluorescens 0-1 expressing AvrRpm1(Pf0-AvrRpm1) Grant et al.56 N/A P. fluorescens 0-1 expressing XopQ (Pf0-XopQ) Schultink et al.43 N/A Biological samples Arabidopsis thaliana leaves Arabidopsis thaliana N/A Arabidopsis thaliana protoplasts Arabidopsis thaliana N/A Nicotiana benthamiana leaves Nicotiana benthamiana N/A Chemicals, peptides, and recombinant proteins Brefeldin A Sigma-Aldrich Cat# B6542 Cycloheximide Sigma-Aldrich Cat# 239763-M Chitin (NA-COS-Y) Mahdi et al.10 N/A Flagellin epitope flg22 MPIPZ stock N/A Oryzalin Sigma-Aldrich Cat# 36182 Fluo-4 AM AAT Bioquest Cat# 20551 FM4-64 Sigma-Aldrich Cat# SCT127 Critical commercial assays RNeasy Plant Mini Kit QIAGEN Cat# 74904 4x Laemmli Sample Buffer Bio-Rad Cat# 1610747 GFP Selector magnetic beads NanoTag Cat# N0310 Experimental models: Cell lines Sf21 insect cells Invitrogen Cat# 11497013 Human embryonic kidney, HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Arabidopsis: Col-0 MPIPZ stock N/A Arabidopsis: mlkl123 Mahdi et al.10 N/A Arabidopsis: MLKL1-GFP Mahdi et al.10 N/A Arabidopsis: eds1-12 Ordon et al.53 N/A (Continued on next page) e1 Cell Host & Microbe 32, 453–465.e1–e6, April 10, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Arabidopsis: MLKL1-GFP in eds1-12 This paper N/A Arabidopsis: 35S::Helo-GFP in mlkl123 This paper N/A Arabidopsis: 35S::GCaMP3 in Col-0 Vincent et al.55 N/A Arabidopsis: 35S::GCaMP3 in mlkl123 This paper N/A Arabidopsis: 35S::GCaMP3 in nrg1.1,1.2 This paper N/A Nicotiana: WT This paper N/A Nicotiana: eds1a, pad4, sag101a, sag101b Lapin et al.24 N/A Nicotiana: 35S::GCaMP3 in WT DeFalco et al.57 N/A Oligonucleotides See Table S1 for primers This paper N/A Recombinant DNA pUC19-AvrRps4-3xFLAG Xing et al.88 N/A pAMPAT-35S-mClover3 This paper N/A pAMPAT-35S-HeLo-mClover3 This paper N/A pAMPAT-35S-HeLoBrace-mClover3 This paper N/A pAMPAT-35S-HeLoBracePseudokinase-mClover3 This paper N/A pAMPAT-35S-AtMLKL1-mClover3 This paper N/A pAMPAT-35S-BracePseudokinaseID-mClover3 This paper N/A pAMPAT-35S-HeLo-3xHA This paper N/A pAMPAT-35S-HeLoBrace-3xHA This paper N/A pAMPAT-35S-HeLoBracePseudokinase-3xHA This paper N/A pAMPAT-35S-AtMLKL1-3xHA This paper N/A pAMPAT-35S-BracePseudokinaseID-3xHA This paper N/A pXCSG-35S-HB-3xHA This paper N/A pXCSG-35S-HP-3xHA This paper N/A pXCSG-35S-HH-3xHA This paper N/A pXCSG-35S-HH+HP-3xHA This paper N/A pXCSG-35S-HP+HB-3xHA This paper N/A pXCSG-35S-S393D-3xHA This paper N/A pSfinx-mYFP This paper N/A pAMPAT-35S-AtMLKL1-cYFP This paper N/A pESPY-35S-AtSAG101-nYFP This paper N/A pXCSG-AtEDS1-FLAG Lapin et al.24 N/A pXCSG-AtSAG101-FLAG Lapin et al.24 N/A pXCSG-AtNRG1.1-3xHA Lapin et al.24 N/A pXCSG-GUS-FLAG Lapin et al.24 N/A pBIN20-35S-GCaMP3 Vincent et al.55 N/A pMDC7-HeLo-3xHA This paper N/A pGWB517-35S-P19 This paper N/A pGWB517-35S-CMV2b This paper N/A pcDNA 5/FRT/TO- HsMLKL (HeLo+Brace)-FLAG This paper N/A pcDNA 5/FRT/TO- AtMLKL (HeLo)-FLAG This paper N/A pcDNA 5/FRT/TO- AtMLKL (HeLo+Brace)-FLAG This paper N/A Software and algorithms Fiji Schindelin et al.89 https://fiji.sc/ R studio RStudioTeam, 2018 http://www.rstudio.com/ Alfafold2 Jumper et al.49 https://alphafold.com/ Cell Host & Microbe 32, 453–465.e1–e6, April 10, 2024 e2
Article Title: Microglial lipid phosphatase SHIP1 limits complement-mediated synaptic pruning in the healthy developing hippocampus.
Article Snippet: In brief Inpp5d, which encodes the lipid phosphatase SHIP1, is a risk gene for Alzheimer’s disease, but its role in brain development has been poorly studied.. Matera, Compagnion et al. demonstrate that Inpp5d is expressed in microglia during early postnatal brain development, where it limits synaptic pruning in a complement-dependent manner, and that its perturbation during brain development has long-lasting effects on cognitive function.
Protease Inhibitor:Article Title: ArreSTick motif controls β-arrestin-binding stability and extends phosphorylation-dependent β-arrestin interactions to non-receptor proteins.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit anti-b-arrestin2 Cell Signaling Technology Cat#3857S; RRID: AB_2258681 rabbit anti-b-arrestin1 Cell Signaling Technology Cat#30036S; RRID: AB_2798985 HRP-conjugated anti-rabbit Cell Signaling Technology Cat#7074S; RRID: AB_2099233 HRP-conjugated anti-mouse Cell Signaling Technology Cat#7076S; RRID: AB_330924 anti-HTATSF1 Proteintech Cat#20805-I-AP; RRID: AB_10695767 Alexa 488-conjugated secondary goat anti-rabbit antibody Invitrogen Cat#A11034; RRID: AB_2576217 Bacterial and virus strains Supercompetent cells home-made N/A Chemicals, peptides, and recombinant proteins Biotin SERVA Electrophoresis GmbH Cat#15060.03 High Capacity NeutrAvidin-Agarose Resin Thermo Scientific Cat#29204 GFP-Trap Magnetic Agarose resin Chromotek Cat#gtma-20 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat#P1585-5MG Poly-L-lysine Sigma-Aldrich Cat#P8920-100ML Lipofectamine 2000 Invitrogen Cat#52887 DMEM VWR Cat#392-0416 Penicillin/Streptomycin Lonza Cat#DE17-602E Fetal bovine serum Biosera Cat#FB-1090/500 SDS SERVA Cat#20760.03 Plasmocin InvivoGen Cat#MPP-44-02 Coelenterazine h Regis Technologies Cat#1-361304-200 Arginine vasopressin Sigma-Aldrich Cat#V9879-1MG Angiotensin II Sigma-Aldrich Cat#A9525-5x1MG A61603 Tocris Cat#1052 DAPI Sigma-Aldrich Cat#A2547-2ML cOmplete Protease Inhibitor Roche Cat#11836145001 Phosphatase Inhibitor Mixture 3 Sigma-Aldrich Cat#P0044-1ML Sodium deoxycholate (SOC) Sigma-Aldrich Cat#D6750-25G Sodium pyrophosphate Sigma-Aldrich Cat#S-6422 Sodium orthovanadate Sigma-Aldrich Cat#S6508-10G Sodium fluoride Sigma-Aldrich Cat#S7920-100G b-Glycerophosphate Sigma-Aldrich Cat#G9422-100G Triton X-100 Sigma-Aldrich Cat#T8787-100ML Iodoacetamide (IAA) Fluka Chemie GmbH Cat#57670 1,4-Dithiothreitol (DTT) Roche Diagnostics Cat#10 197 777 001 Trypsin Gold, Mass Spectrometry Grade Promega Cat#V5280 Disuccinimidyl suberate (DSS) PIERCE Cat#21555 Immobilon Western chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 Bovine Serum Albumin (BSA) Sigma-Aldrich Cat#A3059-100G Methanol MOLAR Chemical Cat#05730-101-340 Ethanol MOLAR Chemical Cat#02910-101-340 Paraformaldehyde Polysciences Cat#18814-20 (Continued on next page) Cell Reports 43, 114241, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER SOC Invitrogen Cat#15544-034 RapiGest Waters Cat#186001860 Deposited data Western blot original images Mendeley Mendeley Data: https://doi.org/10.17632/j7xhxfzdsx.1 Mass spectrometry data MassIVE MassIVE Data: ftp://massive.ucsd.edu/v06/MSV000092868/ Experimental models: Cell lines HEK 293T ATCC Cat#CRL-3216 HEK 293A parent O’Hayre et al.25 N/A HEK 293A barr1/2-KO O’Hayre et al.25 N/A Recombinant DNA pEYFP-N1 wt-barr2–Venus Gyombolai et al.5 N/A pEYFP-N1 K2A-barr2–Venus Tóth et al.20 N/A pEYFP-N1 wt-barr2–Rluc8 Turu et al.67 N/A pEYFP-N1 K2A-barr2–Rluc8 This paper N/A pEYFP-N1 wt-barr1–Venus Gyombolai et al.5 N/A pEYFP-N1 K2A-barr1–Venus This paper N/A pEYFP-N1 wt-barr1–Rluc8 This paper N/A pEYFP-N1 K2A-barr1–Rluc8 This paper N/A pEGFP-N1 L10–mRFP This paper N/A pEGFP-N1 AT1R-Cterm–Venus This paper N/A pEGFP-N1 AT1R-Cterm-TSTS/A–Venus This paper N/A pEGFP-N1 V2R-Cterm–Venus This paper N/A pEYFP-N1 wt-barr2–TurboID This paper N/A pEYFP-N1 K2A-barr2–TurboID This paper N/A pcDNA3.1+ adrenergic receptor alpha 1A cDNA Resource Center Cat##AR0A1A0001 pCMV6 HTATSF1 Origene Cat#SC114990 pEYFP-N1 GRK5–FLAG This paper N/A pCMV5 barr1 (rat) Dr. Stephen S. G. Ferguson N/A pCMV5 barr2 (rat) Dr. Stephen S. G. Ferguson N/A pEYFP-N1 HTSF1–mNeonGreen This paper N/A pEYFP-N1 HTSF1-ST/AA–mNeonGreen This paper N/A pEYFP-N1 HTSF1–Venus This paper N/A pEYFP-N1 HTSF1-ST/AA–Venus This paper N/A Software and algorithms Byonic https://proteinmetrics.com/byonic/ v3.5.0, Protein Metrics Inc GraphPad Prism 9 https://www.graphpad.com GraphPad Prizm Software MaxQuant https://www.maxquant.org/ software version 1.6.7 Compass Data Analysis software 4.3 Bruker Daltonik GmbH Version 4.3 Python code This paper Zenodo: https://doi.org/10.5281/zenodo.10804718 Cell analysis python code This paper Zenodo: https://doi.org/10.5281/zenodo.10072720 Other 96-well white flat bottom plates Greiner Cat#655083 10 cm cell culture dish Greiner Cat#664160 m-Slide 8 Well Ibidi plate Ibidi GmbH Cat#80826 PVDF transfer membrane Thermo Scientific Cat#88518 18 Cell Reports 43, 114241, May 28, 2024
Mass Spectrometry:Article Title: ArreSTick motif controls β-arrestin-binding stability and extends phosphorylation-dependent β-arrestin interactions to non-receptor proteins.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit anti-b-arrestin2 Cell Signaling Technology Cat#3857S; RRID: AB_2258681 rabbit anti-b-arrestin1 Cell Signaling Technology Cat#30036S; RRID: AB_2798985 HRP-conjugated anti-rabbit Cell Signaling Technology Cat#7074S; RRID: AB_2099233 HRP-conjugated anti-mouse Cell Signaling Technology Cat#7076S; RRID: AB_330924 anti-HTATSF1 Proteintech Cat#20805-I-AP; RRID: AB_10695767 Alexa 488-conjugated secondary goat anti-rabbit antibody Invitrogen Cat#A11034; RRID: AB_2576217 Bacterial and virus strains Supercompetent cells home-made N/A Chemicals, peptides, and recombinant proteins Biotin SERVA Electrophoresis GmbH Cat#15060.03 High Capacity NeutrAvidin-Agarose Resin Thermo Scientific Cat#29204 GFP-Trap Magnetic Agarose resin Chromotek Cat#gtma-20 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat#P1585-5MG Poly-L-lysine Sigma-Aldrich Cat#P8920-100ML Lipofectamine 2000 Invitrogen Cat#52887 DMEM VWR Cat#392-0416 Penicillin/Streptomycin Lonza Cat#DE17-602E Fetal bovine serum Biosera Cat#FB-1090/500 SDS SERVA Cat#20760.03 Plasmocin InvivoGen Cat#MPP-44-02 Coelenterazine h Regis Technologies Cat#1-361304-200 Arginine vasopressin Sigma-Aldrich Cat#V9879-1MG Angiotensin II Sigma-Aldrich Cat#A9525-5x1MG A61603 Tocris Cat#1052 DAPI Sigma-Aldrich Cat#A2547-2ML cOmplete Protease Inhibitor Roche Cat#11836145001 Phosphatase Inhibitor Mixture 3 Sigma-Aldrich Cat#P0044-1ML Sodium deoxycholate (SOC) Sigma-Aldrich Cat#D6750-25G Sodium pyrophosphate Sigma-Aldrich Cat#S-6422 Sodium orthovanadate Sigma-Aldrich Cat#S6508-10G Sodium fluoride Sigma-Aldrich Cat#S7920-100G b-Glycerophosphate Sigma-Aldrich Cat#G9422-100G Triton X-100 Sigma-Aldrich Cat#T8787-100ML Iodoacetamide (IAA) Fluka Chemie GmbH Cat#57670 1,4-Dithiothreitol (DTT) Roche Diagnostics Cat#10 197 777 001 Trypsin Gold, Mass Spectrometry Grade Promega Cat#V5280 Disuccinimidyl suberate (DSS) PIERCE Cat#21555 Immobilon Western chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 Bovine Serum Albumin (BSA) Sigma-Aldrich Cat#A3059-100G Methanol MOLAR Chemical Cat#05730-101-340 Ethanol MOLAR Chemical Cat#02910-101-340 Paraformaldehyde Polysciences Cat#18814-20 (Continued on next page) Cell Reports 43, 114241, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER SOC Invitrogen Cat#15544-034 RapiGest Waters Cat#186001860 Deposited data Western blot original images Mendeley Mendeley Data: https://doi.org/10.17632/j7xhxfzdsx.1 Mass spectrometry data MassIVE MassIVE Data: ftp://massive.ucsd.edu/v06/MSV000092868/ Experimental models: Cell lines HEK 293T ATCC Cat#CRL-3216 HEK 293A parent O’Hayre et al.25 N/A HEK 293A barr1/2-KO O’Hayre et al.25 N/A Recombinant DNA pEYFP-N1 wt-barr2–Venus Gyombolai et al.5 N/A pEYFP-N1 K2A-barr2–Venus Tóth et al.20 N/A pEYFP-N1 wt-barr2–Rluc8 Turu et al.67 N/A pEYFP-N1 K2A-barr2–Rluc8 This paper N/A pEYFP-N1 wt-barr1–Venus Gyombolai et al.5 N/A pEYFP-N1 K2A-barr1–Venus This paper N/A pEYFP-N1 wt-barr1–Rluc8 This paper N/A pEYFP-N1 K2A-barr1–Rluc8 This paper N/A pEGFP-N1 L10–mRFP This paper N/A pEGFP-N1 AT1R-Cterm–Venus This paper N/A pEGFP-N1 AT1R-Cterm-TSTS/A–Venus This paper N/A pEGFP-N1 V2R-Cterm–Venus This paper N/A pEYFP-N1 wt-barr2–TurboID This paper N/A pEYFP-N1 K2A-barr2–TurboID This paper N/A pcDNA3.1+ adrenergic receptor alpha 1A cDNA Resource Center Cat##AR0A1A0001 pCMV6 HTATSF1 Origene Cat#SC114990 pEYFP-N1 GRK5–FLAG This paper N/A pCMV5 barr1 (rat) Dr. Stephen S. G. Ferguson N/A pCMV5 barr2 (rat) Dr. Stephen S. G. Ferguson N/A pEYFP-N1 HTSF1–mNeonGreen This paper N/A pEYFP-N1 HTSF1-ST/AA–mNeonGreen This paper N/A pEYFP-N1 HTSF1–Venus This paper N/A pEYFP-N1 HTSF1-ST/AA–Venus This paper N/A Software and algorithms Byonic https://proteinmetrics.com/byonic/ v3.5.0, Protein Metrics Inc GraphPad Prism 9 https://www.graphpad.com GraphPad Prizm Software MaxQuant https://www.maxquant.org/ software version 1.6.7 Compass Data Analysis software 4.3 Bruker Daltonik GmbH Version 4.3 Python code This paper Zenodo: https://doi.org/10.5281/zenodo.10804718 Cell analysis python code This paper Zenodo: https://doi.org/10.5281/zenodo.10072720 Other 96-well white flat bottom plates Greiner Cat#655083 10 cm cell culture dish Greiner Cat#664160 m-Slide 8 Well Ibidi plate Ibidi GmbH Cat#80826 PVDF transfer membrane Thermo Scientific Cat#88518 18 Cell Reports 43, 114241, May 28, 2024
Western Blot:Article Title: ArreSTick motif controls β-arrestin-binding stability and extends phosphorylation-dependent β-arrestin interactions to non-receptor proteins.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit anti-b-arrestin2 Cell Signaling Technology Cat#3857S; RRID: AB_2258681 rabbit anti-b-arrestin1 Cell Signaling Technology Cat#30036S; RRID: AB_2798985 HRP-conjugated anti-rabbit Cell Signaling Technology Cat#7074S; RRID: AB_2099233 HRP-conjugated anti-mouse Cell Signaling Technology Cat#7076S; RRID: AB_330924 anti-HTATSF1 Proteintech Cat#20805-I-AP; RRID: AB_10695767 Alexa 488-conjugated secondary goat anti-rabbit antibody Invitrogen Cat#A11034; RRID: AB_2576217 Bacterial and virus strains Supercompetent cells home-made N/A Chemicals, peptides, and recombinant proteins Biotin SERVA Electrophoresis GmbH Cat#15060.03 High Capacity NeutrAvidin-Agarose Resin Thermo Scientific Cat#29204 GFP-Trap Magnetic Agarose resin Chromotek Cat#gtma-20 Phorbol 12-myristate 13-acetate (PMA) Sigma-Aldrich Cat#P1585-5MG Poly-L-lysine Sigma-Aldrich Cat#P8920-100ML Lipofectamine 2000 Invitrogen Cat#52887 DMEM VWR Cat#392-0416 Penicillin/Streptomycin Lonza Cat#DE17-602E Fetal bovine serum Biosera Cat#FB-1090/500 SDS SERVA Cat#20760.03 Plasmocin InvivoGen Cat#MPP-44-02 Coelenterazine h Regis Technologies Cat#1-361304-200 Arginine vasopressin Sigma-Aldrich Cat#V9879-1MG Angiotensin II Sigma-Aldrich Cat#A9525-5x1MG A61603 Tocris Cat#1052 DAPI Sigma-Aldrich Cat#A2547-2ML cOmplete Protease Inhibitor Roche Cat#11836145001 Phosphatase Inhibitor Mixture 3 Sigma-Aldrich Cat#P0044-1ML Sodium deoxycholate (SOC) Sigma-Aldrich Cat#D6750-25G Sodium pyrophosphate Sigma-Aldrich Cat#S-6422 Sodium orthovanadate Sigma-Aldrich Cat#S6508-10G Sodium fluoride Sigma-Aldrich Cat#S7920-100G b-Glycerophosphate Sigma-Aldrich Cat#G9422-100G Triton X-100 Sigma-Aldrich Cat#T8787-100ML Iodoacetamide (IAA) Fluka Chemie GmbH Cat#57670 1,4-Dithiothreitol (DTT) Roche Diagnostics Cat#10 197 777 001 Trypsin Gold, Mass Spectrometry Grade Promega Cat#V5280 Disuccinimidyl suberate (DSS) PIERCE Cat#21555 Immobilon Western chemiluminescent HRP Substrate Millipore Cat#WBKLS0500 Bovine Serum Albumin (BSA) Sigma-Aldrich Cat#A3059-100G Methanol MOLAR Chemical Cat#05730-101-340 Ethanol MOLAR Chemical Cat#02910-101-340 Paraformaldehyde Polysciences Cat#18814-20 (Continued on next page) Cell Reports 43, 114241, May 28, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER SOC Invitrogen Cat#15544-034 RapiGest Waters Cat#186001860 Deposited data Western blot original images Mendeley Mendeley Data: https://doi.org/10.17632/j7xhxfzdsx.1 Mass spectrometry data MassIVE MassIVE Data: ftp://massive.ucsd.edu/v06/MSV000092868/ Experimental models: Cell lines HEK 293T ATCC Cat#CRL-3216 HEK 293A parent O’Hayre et al.25 N/A HEK 293A barr1/2-KO O’Hayre et al.25 N/A Recombinant DNA pEYFP-N1 wt-barr2–Venus Gyombolai et al.5 N/A pEYFP-N1 K2A-barr2–Venus Tóth et al.20 N/A pEYFP-N1 wt-barr2–Rluc8 Turu et al.67 N/A pEYFP-N1 K2A-barr2–Rluc8 This paper N/A pEYFP-N1 wt-barr1–Venus Gyombolai et al.5 N/A pEYFP-N1 K2A-barr1–Venus This paper N/A pEYFP-N1 wt-barr1–Rluc8 This paper N/A pEYFP-N1 K2A-barr1–Rluc8 This paper N/A pEGFP-N1 L10–mRFP This paper N/A pEGFP-N1 AT1R-Cterm–Venus This paper N/A pEGFP-N1 AT1R-Cterm-TSTS/A–Venus This paper N/A pEGFP-N1 V2R-Cterm–Venus This paper N/A pEYFP-N1 wt-barr2–TurboID This paper N/A pEYFP-N1 K2A-barr2–TurboID This paper N/A pcDNA3.1+ adrenergic receptor alpha 1A cDNA Resource Center Cat##AR0A1A0001 pCMV6 HTATSF1 Origene Cat#SC114990 pEYFP-N1 GRK5–FLAG This paper N/A pCMV5 barr1 (rat) Dr. Stephen S. G. Ferguson N/A pCMV5 barr2 (rat) Dr. Stephen S. G. Ferguson N/A pEYFP-N1 HTSF1–mNeonGreen This paper N/A pEYFP-N1 HTSF1-ST/AA–mNeonGreen This paper N/A pEYFP-N1 HTSF1–Venus This paper N/A pEYFP-N1 HTSF1-ST/AA–Venus This paper N/A Software and algorithms Byonic https://proteinmetrics.com/byonic/ v3.5.0, Protein Metrics Inc GraphPad Prism 9 https://www.graphpad.com GraphPad Prizm Software MaxQuant https://www.maxquant.org/ software version 1.6.7 Compass Data Analysis software 4.3 Bruker Daltonik GmbH Version 4.3 Python code This paper Zenodo: https://doi.org/10.5281/zenodo.10804718 Cell analysis python code This paper Zenodo: https://doi.org/10.5281/zenodo.10072720 Other 96-well white flat bottom plates Greiner Cat#655083 10 cm cell culture dish Greiner Cat#664160 m-Slide 8 Well Ibidi plate Ibidi GmbH Cat#80826 PVDF transfer membrane Thermo Scientific Cat#88518 18 Cell Reports 43, 114241, May 28, 2024
Expressing:Article Title: Cytoplasmic calcium influx mediated by plant MLKLs confers TNL-triggered immunity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat Monoclonal Anti-HA Sigma-Aldrich Cat# 11867423001 Goat Anti-Rat Sigma-Aldrich Cat# AP136P Rabbit Polyclonal Anti-GFP Abcam Cat# ab6556 Goat Anti-Rabbit Sigma-Aldrich Cat# A9169 Mouse Monoclonal Anti-FLAG Sigma-Aldrich Cat# F1804 Goat Anti-Mouse Sigma-Aldrich Cat# A9316 Horseradish peroxidase (HRP)-coupled Anti-DYKDDDDK Miltenyi Biotec Cat# 130-101-572 Horseradish peroxidase (HRP)-coupled Anti-HA Miltenyi Biotec Cat# 130-091-972 Mouse monoclonal Anti- Alpha-Tubulin Sigma-Aldrich Cat# T6074 HRP-coupled Anti-mouse Cell Signaling Technology Cat# 7076S Bacterial and virus strains Chemically Competent E. coli MPIPZ stock N/A Electrically Competent A. tumefaciens GV3101 (pMP90RK or pMP90Rgent) MPIPZ stock N/A Pseudomonas syringae pv. tomato (Pst) DC3000 Mahdi et al.10 N/A Xanthomonas campestris pv vesicatoria (Xcv 85-10) Thieme et al.87 N/A P. fluorescens 0-1 expressing empty vector (Pf0-EV) Saucet et al.42 N/A P. fluorescens 0-1 expressing AvrRps4 (Pf0-AvrRps4) Saucet et al.42 N/A P. fluorescens 0-1 expressing AvrRpm1(Pf0-AvrRpm1) Grant et al.56 N/A P. fluorescens 0-1 expressing XopQ (Pf0-XopQ) Schultink et al.43 N/A Biological samples Arabidopsis thaliana leaves Arabidopsis thaliana N/A Arabidopsis thaliana protoplasts Arabidopsis thaliana N/A Nicotiana benthamiana leaves Nicotiana benthamiana N/A Chemicals, peptides, and recombinant proteins Brefeldin A Sigma-Aldrich Cat# B6542 Cycloheximide Sigma-Aldrich Cat# 239763-M Chitin (NA-COS-Y) Mahdi et al.10 N/A Flagellin epitope flg22 MPIPZ stock N/A Oryzalin Sigma-Aldrich Cat# 36182 Fluo-4 AM AAT Bioquest Cat# 20551 FM4-64 Sigma-Aldrich Cat# SCT127 Critical commercial assays RNeasy Plant Mini Kit QIAGEN Cat# 74904 4x Laemmli Sample Buffer Bio-Rad Cat# 1610747 GFP Selector magnetic beads NanoTag Cat# N0310 Experimental models: Cell lines Sf21 insect cells Invitrogen Cat# 11497013 Human embryonic kidney, HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Arabidopsis: Col-0 MPIPZ stock N/A Arabidopsis: mlkl123 Mahdi et al.10 N/A Arabidopsis: MLKL1-GFP Mahdi et al.10 N/A Arabidopsis: eds1-12 Ordon et al.53 N/A (Continued on next page) e1 Cell Host & Microbe 32, 453–465.e1–e6, April 10, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Arabidopsis: MLKL1-GFP in eds1-12 This paper N/A Arabidopsis: 35S::Helo-GFP in mlkl123 This paper N/A Arabidopsis: 35S::GCaMP3 in Col-0 Vincent et al.55 N/A Arabidopsis: 35S::GCaMP3 in mlkl123 This paper N/A Arabidopsis: 35S::GCaMP3 in nrg1.1,1.2 This paper N/A Nicotiana: WT This paper N/A Nicotiana: eds1a, pad4, sag101a, sag101b Lapin et al.24 N/A Nicotiana: 35S::GCaMP3 in WT DeFalco et al.57 N/A Oligonucleotides See Table S1 for primers This paper N/A Recombinant DNA pUC19-AvrRps4-3xFLAG Xing et al.88 N/A pAMPAT-35S-mClover3 This paper N/A pAMPAT-35S-HeLo-mClover3 This paper N/A pAMPAT-35S-HeLoBrace-mClover3 This paper N/A pAMPAT-35S-HeLoBracePseudokinase-mClover3 This paper N/A pAMPAT-35S-AtMLKL1-mClover3 This paper N/A pAMPAT-35S-BracePseudokinaseID-mClover3 This paper N/A pAMPAT-35S-HeLo-3xHA This paper N/A pAMPAT-35S-HeLoBrace-3xHA This paper N/A pAMPAT-35S-HeLoBracePseudokinase-3xHA This paper N/A pAMPAT-35S-AtMLKL1-3xHA This paper N/A pAMPAT-35S-BracePseudokinaseID-3xHA This paper N/A pXCSG-35S-HB-3xHA This paper N/A pXCSG-35S-HP-3xHA This paper N/A pXCSG-35S-HH-3xHA This paper N/A pXCSG-35S-HH+HP-3xHA This paper N/A pXCSG-35S-HP+HB-3xHA This paper N/A pXCSG-35S-S393D-3xHA This paper N/A pSfinx-mYFP This paper N/A pAMPAT-35S-AtMLKL1-cYFP This paper N/A pESPY-35S-AtSAG101-nYFP This paper N/A pXCSG-AtEDS1-FLAG Lapin et al.24 N/A pXCSG-AtSAG101-FLAG Lapin et al.24 N/A pXCSG-AtNRG1.1-3xHA Lapin et al.24 N/A pXCSG-GUS-FLAG Lapin et al.24 N/A pBIN20-35S-GCaMP3 Vincent et al.55 N/A pMDC7-HeLo-3xHA This paper N/A pGWB517-35S-P19 This paper N/A pGWB517-35S-CMV2b This paper N/A pcDNA 5/FRT/TO- HsMLKL (HeLo+Brace)-FLAG This paper N/A pcDNA 5/FRT/TO- AtMLKL (HeLo)-FLAG This paper N/A pcDNA 5/FRT/TO- AtMLKL (HeLo+Brace)-FLAG This paper N/A Software and algorithms Fiji Schindelin et al.89 https://fiji.sc/ R studio RStudioTeam, 2018 http://www.rstudio.com/ Alfafold2 Jumper et al.49 https://alphafold.com/ Cell Host & Microbe 32, 453–465.e1–e6, April 10, 2024 e2
Magnetic Beads:Article Title: Cytoplasmic calcium influx mediated by plant MLKLs confers TNL-triggered immunity.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat Monoclonal Anti-HA Sigma-Aldrich Cat# 11867423001 Goat Anti-Rat Sigma-Aldrich Cat# AP136P Rabbit Polyclonal Anti-GFP Abcam Cat# ab6556 Goat Anti-Rabbit Sigma-Aldrich Cat# A9169 Mouse Monoclonal Anti-FLAG Sigma-Aldrich Cat# F1804 Goat Anti-Mouse Sigma-Aldrich Cat# A9316 Horseradish peroxidase (HRP)-coupled Anti-DYKDDDDK Miltenyi Biotec Cat# 130-101-572 Horseradish peroxidase (HRP)-coupled Anti-HA Miltenyi Biotec Cat# 130-091-972 Mouse monoclonal Anti- Alpha-Tubulin Sigma-Aldrich Cat# T6074 HRP-coupled Anti-mouse Cell Signaling Technology Cat# 7076S Bacterial and virus strains Chemically Competent E. coli MPIPZ stock N/A Electrically Competent A. tumefaciens GV3101 (pMP90RK or pMP90Rgent) MPIPZ stock N/A Pseudomonas syringae pv. tomato (Pst) DC3000 Mahdi et al.10 N/A Xanthomonas campestris pv vesicatoria (Xcv 85-10) Thieme et al.87 N/A P. fluorescens 0-1 expressing empty vector (Pf0-EV) Saucet et al.42 N/A P. fluorescens 0-1 expressing AvrRps4 (Pf0-AvrRps4) Saucet et al.42 N/A P. fluorescens 0-1 expressing AvrRpm1(Pf0-AvrRpm1) Grant et al.56 N/A P. fluorescens 0-1 expressing XopQ (Pf0-XopQ) Schultink et al.43 N/A Biological samples Arabidopsis thaliana leaves Arabidopsis thaliana N/A Arabidopsis thaliana protoplasts Arabidopsis thaliana N/A Nicotiana benthamiana leaves Nicotiana benthamiana N/A Chemicals, peptides, and recombinant proteins Brefeldin A Sigma-Aldrich Cat# B6542 Cycloheximide Sigma-Aldrich Cat# 239763-M Chitin (NA-COS-Y) Mahdi et al.10 N/A Flagellin epitope flg22 MPIPZ stock N/A Oryzalin Sigma-Aldrich Cat# 36182 Fluo-4 AM AAT Bioquest Cat# 20551 FM4-64 Sigma-Aldrich Cat# SCT127 Critical commercial assays RNeasy Plant Mini Kit QIAGEN Cat# 74904 4x Laemmli Sample Buffer Bio-Rad Cat# 1610747 GFP Selector magnetic beads NanoTag Cat# N0310 Experimental models: Cell lines Sf21 insect cells Invitrogen Cat# 11497013 Human embryonic kidney, HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Arabidopsis: Col-0 MPIPZ stock N/A Arabidopsis: mlkl123 Mahdi et al.10 N/A Arabidopsis: MLKL1-GFP Mahdi et al.10 N/A Arabidopsis: eds1-12 Ordon et al.53 N/A (Continued on next page) e1 Cell Host & Microbe 32, 453–465.e1–e6, April 10, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Arabidopsis: MLKL1-GFP in eds1-12 This paper N/A Arabidopsis: 35S::Helo-GFP in mlkl123 This paper N/A Arabidopsis: 35S::GCaMP3 in Col-0 Vincent et al.55 N/A Arabidopsis: 35S::GCaMP3 in mlkl123 This paper N/A Arabidopsis: 35S::GCaMP3 in nrg1.1,1.2 This paper N/A Nicotiana: WT This paper N/A Nicotiana: eds1a, pad4, sag101a, sag101b Lapin et al.24 N/A Nicotiana: 35S::GCaMP3 in WT DeFalco et al.57 N/A Oligonucleotides See Table S1 for primers This paper N/A Recombinant DNA pUC19-AvrRps4-3xFLAG Xing et al.88 N/A pAMPAT-35S-mClover3 This paper N/A pAMPAT-35S-HeLo-mClover3 This paper N/A pAMPAT-35S-HeLoBrace-mClover3 This paper N/A pAMPAT-35S-HeLoBracePseudokinase-mClover3 This paper N/A pAMPAT-35S-AtMLKL1-mClover3 This paper N/A pAMPAT-35S-BracePseudokinaseID-mClover3 This paper N/A pAMPAT-35S-HeLo-3xHA This paper N/A pAMPAT-35S-HeLoBrace-3xHA This paper N/A pAMPAT-35S-HeLoBracePseudokinase-3xHA This paper N/A pAMPAT-35S-AtMLKL1-3xHA This paper N/A pAMPAT-35S-BracePseudokinaseID-3xHA This paper N/A pXCSG-35S-HB-3xHA This paper N/A pXCSG-35S-HP-3xHA This paper N/A pXCSG-35S-HH-3xHA This paper N/A pXCSG-35S-HH+HP-3xHA This paper N/A pXCSG-35S-HP+HB-3xHA This paper N/A pXCSG-35S-S393D-3xHA This paper N/A pSfinx-mYFP This paper N/A pAMPAT-35S-AtMLKL1-cYFP This paper N/A pESPY-35S-AtSAG101-nYFP This paper N/A pXCSG-AtEDS1-FLAG Lapin et al.24 N/A pXCSG-AtSAG101-FLAG Lapin et al.24 N/A pXCSG-AtNRG1.1-3xHA Lapin et al.24 N/A pXCSG-GUS-FLAG Lapin et al.24 N/A pBIN20-35S-GCaMP3 Vincent et al.55 N/A pMDC7-HeLo-3xHA This paper N/A pGWB517-35S-P19 This paper N/A pGWB517-35S-CMV2b This paper N/A pcDNA 5/FRT/TO- HsMLKL (HeLo+Brace)-FLAG This paper N/A pcDNA 5/FRT/TO- AtMLKL (HeLo)-FLAG This paper N/A pcDNA 5/FRT/TO- AtMLKL (HeLo+Brace)-FLAG This paper N/A Software and algorithms Fiji Schindelin et al.89 https://fiji.sc/ R studio RStudioTeam, 2018 http://www.rstudio.com/ Alfafold2 Jumper et al.49 https://alphafold.com/ Cell Host & Microbe 32, 453–465.e1–e6, April 10, 2024 e2
Bioprocessing:Article Title: Microglial lipid phosphatase SHIP1 limits complement-mediated synaptic pruning in the healthy developing hippocampus.
Article Snippet: In brief Inpp5d, which encodes the lipid phosphatase SHIP1, is a risk gene for Alzheimer’s disease, but its role in brain development has been poorly studied.. Matera, Compagnion et al. demonstrate that Inpp5d is expressed in microglia during early postnatal brain development, where it limits synaptic pruning in a complement-dependent manner, and that its perturbation during brain development has long-lasting effects on cognitive function.
Imaging:
Staining:
Transfection:
SYBR Green Assay:
DC Protein Assay:
Control:Article Title: Nuclear and cytosolic fractions of SOX2 synergize as transcriptional and translational co-regulators of cell fate.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal (D6D9) anti-SOX2 Cell Signaling Technology Cat#3579; RRID:AB_2195767 Rabbit monoclonal (D8G8H) anti-SOX9 Cell Signaling Technology Cat#82630; RRID:AB_2665492 Rabbit polyclonal anti-OCT4 (aka POU5F1) Cell Signaling Technology Cat#2750; RRID:AB_823583 Rabbit polyclonal anti-KLF4 Cell Signaling Technology Cat#4038; RRID:AB_2265207 Rabbit monoclonal (D84C12) anti-cMYC Cell Signaling Technology Cat#5605; RRID:AB_1903938 Rabbit monoclonal (5G10) anti-RPS6 Cell Signaling Technology Cat#2217; RRID:AB_331355 Rabbit monoclonal (2F9) anti-pRPS6 (Ser235/236) Cell Signaling Technology Cat#4856; RRID:AB_2181037 Rabbit monoclonal (D68F8) anti-pRPS6 (Ser240/244) Cell Signaling Technology Cat#5364; RRID:AB_10694233 Rabbit monoclonal (C67E7) anti-panAKT Cell Signaling Technology Cat#4691; RRID:AB_915783 Rabbit monoclonal (D9E) anti-pAKT (Ser473) Cell Signaling Technology Cat#4060; RRID:AB_2315049 Rabbit monoclonal (108E2) anti-pS6K1 (Thr389) Cell Signaling Technology Cat#9234; RRID:AB_2269803 Rabbit monoclonal (D4B8) anti-ATF4 Cell Signaling Technology Cat#11815; RRID:AB_2616025 Rabbit monoclonal (D64F1) anti-CHOP Cell Signaling Technology Cat#5554; RRID:AB_10694399 Rabbit polyclonal anti-eIF2alpha Cell Signaling Technology Cat#9722; RRID:AB_2230924 Rabbit monoclonal (119A11) anti-peIF2alpha (Ser51) Cell Signaling Technology Cat#3597; RRID:AB_390740 Rabbit monoclonal (12D1) anti-p21 (aka Waf1/Cip1) Cell Signaling Technology Cat#2947; RRID:AB_823586 Rabbit monoclonal (D1H1) anti-H3 Cell Signaling Technology Cat#4499; RRID:AB_10544537 Rabbit monoclonal (D16H11) anti-GAPDH Cell Signaling Technology Cat#5174 Rabbit monoclonal (8H10D10) anti-beta-actin Cell Signaling Technology Cat#3700; RRID:AB_10622025 Rabbit monoclonal (9F3) anti-beta-tubulin Cell Signaling Technology Cat#2128; RRID:AB_823664 Rabbit polyclonal anti-RPL3 Abcam ab154882 Rabbit polyclonal anti-RPL23 Sigma-Aldrich HPA003373; RRID:AB_1856436 Mouse monoclonal anti-mCherry Clontech, TakaRa Bio Living Colors #632543; RRID:AB_2307319 Mouse monoclonal (9E10) anti-cMyc Invitrogen #13-2500; RRID:AB_2533008 HRP-linked anti-rabbit Cell Signaling Technology Cat#7074; RRID:AB_2099233 (Continued on next page) Cell Reports 43, 114807, October 22, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER HRP-linked anti-mouse Cell Signaling Technology Cat7076; RRID:AB_330924 Streptavidin-HRP conjugate R&D Systems #890803 isotype control (official product name: ‘‘Normal’’ rabbit IgG) Santa Cruz Biotechnology sc-3888; RRID:AB_145841 Bacterial and virus strains OneShotTM chemically competent TOP10 E.coli Thermo-Fisher C404003 Biological samples No primary biological samples were used in this study. .. Chemicals, peptides, and recombinant proteins Cycloheximide Sigma C7698 Puromycin Applichem A2856 Geneticin Gibco #11-811-031 O-propargyl-puromycin (OPP) Thermo-Fisher Click-iT Plus OPP, C10456 Oligomycin Sigma #75351 2-Deoxy-D-glucose Sigma D3179 2-Nitrobenzyl-desoxyglucose (2-NBDG) Thermo-Fisher N13195 Carbonyl-cyanide-4-(trifluoromethoxy)phenylhydrazone (FCCP) Sigma C2920 Rotenone Sigma R8875 Biotin Sigma B4639 Heparin Ratiopharm #06884371 Insulin Lonza CC-4021G Hydrocortisone Lonza CC-4031G Epidermal growth factor (EGF) Sigma E9644 Fibroblast growth factor (FGF) PeproTech #100-18B Recombinant human SOX2 Novus Biologicals NBP2-35268 Critical commercial assays FluoroTect GreenLys in vitro Translation Labeling System Promega #L5001 Click-iTTM Plus OPP Alexa FluorTM 488 Protein Synthesis Assay Kit Thermo-Fisher C10456 SMARTer smRNA-Seq Kit for Illumina Clontech, Takara Bio #635031 TruSeq Stranded Total RNA Kit V2.0 Illumina #20020594 Deposited data RNAseq raw sequencing data This paper ArrayExpress (https://www.ebi.ac.uk/ biostudies/arrayexpress) Record number: E-MTAB-13098 RIBOseq raw sequencing data This paper ArrayExpress (https://www.ebi.ac.uk/ biostudies/arrayexpress) Record number: E-MTAB-13099 RNAseq and RIBOseq analysis scripts This paper Zenodo (https://zenodo.org/) https://doi.org/10.5281/zenodo.13752731 MS hit lists This paper PRIDE (https://www.ebi.ac.uk./pride/, Dataset identifier: PXD015157 and https://doi.org/10.6019/PXD015157. (Continued on next page) 22 Cell Reports 43, 114807, October 22, 2024
|
Cell Signaling Technology Inc is a verified supplier 
Cell Signaling Technology Inc manufactures this product 