Recombinant:Article Title: Selective removal of astrocytic PERK protects against glymphatic impairment and decreases toxic aggregation of β-amyloid and tau.
Article Snippet: Article Selective removal of astrocytic PERK protects against glymphatic impairment and decreases toxic aggregation of β-amyloid and tau Highlights • Astrocyte-specific PERK deletion restores protein synthesis and glymphatic function • Removal of astrocytic PERK reduces Aβ and tau aggregation • Cognitive performance is improved after astrocytic PERK deletion • Chronic PERK signaling disrupts perivascular AQP4 localization via CK2 Authors Kai Chen, Yosuke M. Morizawa, Tal Nuriel, Osama Al-Dalahmah, Zhongcong Xie, Guang Yang Correspondence zhongcong.Xie@uth.tmc.edu (Z.X.), gy2268@cumc.columbia.edu (G.Y.). In brief Chen et al. show that in AD mouse models, chronic activation of astrocytic PERK-eIF2a signaling suppresses protein synthesis and disrupts perivascular AQP4 localization via CK2- dependent mechanisms.. Inhibiting astrocytic PERK restores glymphatic function, reduces AD-related pathology, and improves cognitive performance.
Article Title: A brainstem to hypothalamic arcuate nucleus GABAergic circuit drives feeding.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit ani-c-Fos antibody Cell Signaling Cat#2250; RRID:AB_2247211 Rabbit anti-c-Fos antibody Merk Cat#ABE457; RRID:AB_2631318 Goat anti-mCherry antibody Scigen Cat#AB0040-200; RRID:AB_2333093 Rabbit anti-hrGFP antibody Agilent Cat#240141; RRID:AB_10596971 Rabitt anti-POMC antibody Phoenix Pharmaceuticals Cat#H-029-30; RRID:AB_2307442 Rabbit anti-RFP antibody Rockland Immunochemicals Cat#600-401-379; RRID:AB_2209751 Donkey anti-rabbit AlexaFluor 488 antibody Invitrogen Cat#A78948; RRID:AB_2921070 Donkey anti-chicken AlexaFluor 488 antibody Jackson immunoresearch Cat# 703-545-155; RRID:AB_2340375 Donkey anti-rabbit AlexaFluor 594 antibody Invitrogen Cat#A-21207; RRID:AB_141637 Donkey anti-goat AlexaFluor 594 antibody Invitrogen Cat#A-11058; RRID:AB_2534105 Donkey anti-goat Biotin-SP Jackson immunoresearch Cat# 711-065-152; RRID:AB_2340593 Bacterial and virus strains AAV8-hSyn-DIO-hM3D(Gq)-mCherry Addgene Cat#44361-AAV8; RRID:Addgene_44361 AAV8-hSyn-DIO-hM4D(Gi)-mCherry Addgene Cat#44362-AAV8; RRID:Addgene_44362 AAVrg-hSyn-fDIO-hM3D (Gq)-mCherry-WPREpA Addgene Cat#154868-AAVrg; RRID:Addgene_154868 AAV8-hSyn-DIO-mCherry Addgene Cat#50459-AAV8; RRID:Addgene_50459 AAV8-pEF1a-DIO-FLPo-WPRE-hGHpA Addgene Cat#87306-AAV8; RRID:Addgene_87306 AAV2-EF1a-DIO-ChR2 (E123T/T159C)-mCherry University of North Carolina Vector Core N/A AAV2-EF1a-DIO-ChR2 (E123T/T159C)-YFP University of North Carolina Vector Core N/A Chemicals, peptides, and recombinant proteins Clozapine-N-Oxide Tocris Cat#4936 Liraglutide Tocris Cat#6517 Ghrelin Tocris Cat#1463 Gabazine Tocris Cat#1262 GABA Tocris Cat#0344 CGP-55845 Tocris Cat#1248 MDL-72222 Tocris Cat#0640 QX-314 Tocris Cat#2313 ImmPACT DAB Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4105 VECTASTAIN ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-4000 Experimental models: Organisms/strains Mouse: Slc32a1tm2(cre)Lowl The Jackson Laboratory Cat#016962; RRID:IMSR_JAX:016962 Mouse: B6.FVB-Tg(Npy-hrGFP)1Lowl/J The Jackson Laboratory Cat#006417; RRID:IMSR_JAX:006417 Mouse: B6.Cg-Gt(ROSA)26Sortm9 (CAG-tdTomato)Hze/J The Jackson Laboratory Cat#007909; RRID:IMSR_JAX:007909 Mouse: Tg(Pomc-DsRed)18Low Prof. Malcom Low (University of Michigan) Hentges et al.75 Software and algorithms Prism 10 GraphPad Software https://www.graphpad.com/ RRID:SCR_002798 ImageJ NIH https://imagej.net/ij/RRID:SCR_003070 Affinity Designer 2 Serif https://affinity.serif.com/ (Continued on next page) e1 Current Biology 34, 1–11.e1–e4, April 22, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Arduino IDE Arduino https://www.arduino.cc/ RRID:SCR_024884 ANYmaze Stoelting https://www.any-maze.com/ RRID:SCR_014289 Phenomaster TSE-Systems https://www.tse-systems.com/ Axiovision Zen https://www.micro-shop.zeiss.com/ RRID:SCR_002677 RNAseq data Data are available from the NCBI Gene Expression Omnibus Accession GSE168737 Other 473-nm laser Laserglow Cat#LRS-0473 Optic fibers 200um, 0.39NA Thorlabs Cat#CFMLC Patch cables Thorlabs Cat#M83L1 Microinjector Narishige Cat#IM-11-2
Enzyme-linked Immunosorbent Assay:Article Title: Selective removal of astrocytic PERK protects against glymphatic impairment and decreases toxic aggregation of β-amyloid and tau.
Article Snippet: Article Selective removal of astrocytic PERK protects against glymphatic impairment and decreases toxic aggregation of β-amyloid and tau Highlights • Astrocyte-specific PERK deletion restores protein synthesis and glymphatic function • Removal of astrocytic PERK reduces Aβ and tau aggregation • Cognitive performance is improved after astrocytic PERK deletion • Chronic PERK signaling disrupts perivascular AQP4 localization via CK2 Authors Kai Chen, Yosuke M. Morizawa, Tal Nuriel, Osama Al-Dalahmah, Zhongcong Xie, Guang Yang Correspondence zhongcong.Xie@uth.tmc.edu (Z.X.), gy2268@cumc.columbia.edu (G.Y.). In brief Chen et al. show that in AD mouse models, chronic activation of astrocytic PERK-eIF2a signaling suppresses protein synthesis and disrupts perivascular AQP4 localization via CK2- dependent mechanisms.. Inhibiting astrocytic PERK restores glymphatic function, reduces AD-related pathology, and improves cognitive performance.
Article Title: Lcn2 from neutrophil extracellular traps induces astrogliosis and post-stroke emotional disorders.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GFAP Millipore Cat#ab5541; RRID: AB_177521 Anti-Iba-1 Novus Biologicals Cat#nb100-1028; RRID: AB_3148646 Anti-MPO Proteintech Cat#66177-1-Ig; RRID: AB_2881572 Anti-citH3 Abcam Cat#ab281584; RRID: AB_3697176 Anti-Ly6G Abcam Cat#ab25377; RRID: AB_470492 Anti-S100β Proteintech Cat#15146-1-AP; RRID: AB_2254244 Anti-Lcn2 Novus Cat#AF1857; RRID: AB_355022 Anti-CD31 Novus Cat#NB100-2284; RRID: AB_10002513 Anti-ZO-1 Proteintech Cat#21773-1-AP; RRID: AB_10733242 Anti-NeuN Sigma-Aldrich Cat#ABN90; RRID: AB_3696646 Anti-Ly6G BD Biosciences Cat#560599; RRID: AB_1727560 Alexa Fluor® 555 AffiniPureTM Donkey Anti-Rat IgG (H+L) Jackson ImmunoResearch Cat#712-565-150; RRID: AB_3095473 Alexa Fluor® 555 AffiniPureTM Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-565-150; RRID: AB_3095479 Alexa Fluor® 488 AffiniPureTM Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-545-150; RRID: AB_2340846 Alexa Fluor 488-conjugated AffiniPureTM Donkey Anti-Rabbit IgG Jackson ImmunoResearch Cat#711-545-152; RRID: AB_2313584 Donkey anti-Rabbit IgG (H+L) Secondary Antibody, Alexa FluorTM 555 Invitrogen Cat#A-31572; RRID: AB_162543 Donkey anti-Goat IgG (H+L) Secondary Antibody, Alexa FluorTM 594 Invitrogen Cat#A-11058; RRID: AB_2534105 Donkey anti-Goat IgG (H+L) Secondary Antibody, Alexa FluorTM Plus 488 Invitrogen Cat#A32814; RRID: AB_2762838 Alexa Fluor® 488 AffiniPureTM Donkey Anti-Chicken IgY (IgG) (H+L) Jackson ImmunoResearch Cat#703-545-155; RRID: AB_2340375 Alexa Fluor® 647 AffiniPureTM Donkey Anti-Chicken IgY (IgG) (H+L) Jackson ImmunoResearch Cat#703-605-155; RRID: AB_2340379 Bacterial and virus strains rAAV-GfaABC1D-GCaMP6f Braincase Cat#BC-0378 rAAV-Ef1α-DIO-hM3D(Gq)-mCherry Braincase Cat#BC-0146 rAAV-Ef1α-DIO-mCherry Braincase Cat#BC-0016 Biological samples Serum samples from patients Shanghai Yang Zhi Rehabilitation Hospital This paper Chemicals, peptides, and recombinant proteins Rose Bengal Sigma Cat#198250 Tamoxifen Sigma Cat#579000 DAPI Beyotime Cat#C1006 Fixable Viability Stain 510 BD Biosciences Cat#564406 Percoll Sigma Cat#P4937 PLX5622, AIN-6A SYSE Biotechnology Cat#D20010801 Phorbol myristate acetate Sigma Cat#524400 (Continued on next page) Neuron 113, 4199–4216.e1–e8, December 17, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Ionomycin Sigma Cat#I3909 Carprofen Sigma Cat#PHR1452 Dexamethasone MedChemExpress Cat#HY-14686 Enrofloxacin MedChemExpress Cat#HY-B0502 Pentobarbital sodium Sigma Cat#11715 Isoflurane Ruiwode Cat#R510-22-10 Evan’s blue Sigma Cat#E2129 Critical commercial assays RNAscopeTM Multiplex Fluorescent Reagent Kit v2 Advanced Cell Diagnostics Cat#323100 VECTASTAIN® Elite® ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 TSA Vivid Fluorophore 520 Advanced Cell Diagnostics Cat#PG-323271 TSA Vwid Fluorophore 650 Advanced Cell Diagnostics Cat#PG-323273 RNAscope Target RetrievalReagents Advanced Cell Diagnostics Cat#322000 RNAscope Probe Diluent Advanced Cell Diagnostics Cat#300041 Human MPO-DNA ELISA KIT jingkang Cat#JLC-Y4628 Human citH3-DNA ELISA KIT jingkang Cat#JLC87163 Mouse MPO-DNA ELISA KIT jingkang Cat#JLC87162 Mouse citH3-DNA ELISA KIT jingkang Cat#JLC87164 Experimental models: Organisms/strains C57BL/6 GemPharmatech Cat#N000013; RRID: IMSR_GPT: N000013 Lcn2 KO GemPharmatech Cat#T014584; RRID: IMSR_GPT: T014584 Lcn2loxP/loxP Shanghai Model Organisms Center Cat#NM-CKO-00134; RRID: IMSR_NM-CKO-00134 Ly6G-iCreERT2 Shanghai Model Organisms Center Cat#NM-KI-200218; RRID: IMSR_NM-KI-200218 Aldh1l1-CreERT2::Ai14 Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University This paper GFAP-iCreERT2 Jackson Laboratories Cat#012849; RRID: IMSR_JAK: 012849 RCL-GCaMP6s Jackson Laboratories Cat#028866; RRID: IMSR_JAX:028866 Pad4 KO Shanghai Model Organisms Center Cat#NM-KO-190334; RRID: IMSR_NM-KO-190334 Pad4-Flox/Ly6G-Cre-2A-tdTomato Shanghai Model Organisms Center Cat#NM-CKO-234151; RRID: IMSR_NM-CKO- 234151 Aldh1l1-Cre Jackson Laboratories Cat#023748; RRID: IMSR_JAX: 023748 Cx3cr1-GFP Jackson Laboratories Cat#005582; RRID: IMSR JAX: 005582 Oligonucleotides RNAscopeTM Probe- Mm-Padi4-C2 Advanced Cell Diagnostics Cat#467591-C2 RNAscopeTM Probe- Mm-Lcn2-C3 Advanced Cell Diagnostics Cat#313971-C3 Software and algorithms MATLAB R2014b Mathworks RRID: SCR_001622 FIJI ImageJ RRID: SCR_002285 Olympus FluoView Olympus RRID: SCR_014215 GraphPad Prism 8.0 GraphPad RRID: SCR_002798 IMARIS Oxford Instruments Group RRID: SCR_007274 Adobe Illustrator Adobe Systems RRID: SCR_010279 R (version 4.2.1) R Project https://www.r-project.org FlowJo software BD Biosciences RRID: SCR_000410 e2 Neuron 113, 4199–4216.e1–e8, December 17, 2025 ..
Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) e2 Immunity 57, 1–14.e1–e10, July 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) Immunity 57, 1–14.e1–e10, July 9, 2024 e3
Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) ll OPEN ACCESSArticle Immunity 57, 1696–1709.e1–e10, July 9, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) ll OPEN ACCESS Article e3 Immunity 57, 1696–1709.e1–e10, July 9, 2024
Bicinchoninic Acid Protein Assay:Article Title: Selective removal of astrocytic PERK protects against glymphatic impairment and decreases toxic aggregation of β-amyloid and tau.
Article Snippet: Article Selective removal of astrocytic PERK protects against glymphatic impairment and decreases toxic aggregation of β-amyloid and tau Highlights • Astrocyte-specific PERK deletion restores protein synthesis and glymphatic function • Removal of astrocytic PERK reduces Aβ and tau aggregation • Cognitive performance is improved after astrocytic PERK deletion • Chronic PERK signaling disrupts perivascular AQP4 localization via CK2 Authors Kai Chen, Yosuke M. Morizawa, Tal Nuriel, Osama Al-Dalahmah, Zhongcong Xie, Guang Yang Correspondence zhongcong.Xie@uth.tmc.edu (Z.X.), gy2268@cumc.columbia.edu (G.Y.). In brief Chen et al. show that in AD mouse models, chronic activation of astrocytic PERK-eIF2a signaling suppresses protein synthesis and disrupts perivascular AQP4 localization via CK2- dependent mechanisms.. Inhibiting astrocytic PERK restores glymphatic function, reduces AD-related pathology, and improves cognitive performance.
Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) e2 Immunity 57, 1–14.e1–e10, July 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) Immunity 57, 1–14.e1–e10, July 9, 2024 e3
Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) ll OPEN ACCESSArticle Immunity 57, 1696–1709.e1–e10, July 9, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) ll OPEN ACCESS Article e3 Immunity 57, 1696–1709.e1–e10, July 9, 2024
Multiplex Assay:Article Title: Selective removal of astrocytic PERK protects against glymphatic impairment and decreases toxic aggregation of β-amyloid and tau.
Article Snippet: Article Selective removal of astrocytic PERK protects against glymphatic impairment and decreases toxic aggregation of β-amyloid and tau Highlights • Astrocyte-specific PERK deletion restores protein synthesis and glymphatic function • Removal of astrocytic PERK reduces Aβ and tau aggregation • Cognitive performance is improved after astrocytic PERK deletion • Chronic PERK signaling disrupts perivascular AQP4 localization via CK2 Authors Kai Chen, Yosuke M. Morizawa, Tal Nuriel, Osama Al-Dalahmah, Zhongcong Xie, Guang Yang Correspondence zhongcong.Xie@uth.tmc.edu (Z.X.), gy2268@cumc.columbia.edu (G.Y.). In brief Chen et al. show that in AD mouse models, chronic activation of astrocytic PERK-eIF2a signaling suppresses protein synthesis and disrupts perivascular AQP4 localization via CK2- dependent mechanisms.. Inhibiting astrocytic PERK restores glymphatic function, reduces AD-related pathology, and improves cognitive performance.
Article Title: Lcn2 from neutrophil extracellular traps induces astrogliosis and post-stroke emotional disorders.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GFAP Millipore Cat#ab5541; RRID: AB_177521 Anti-Iba-1 Novus Biologicals Cat#nb100-1028; RRID: AB_3148646 Anti-MPO Proteintech Cat#66177-1-Ig; RRID: AB_2881572 Anti-citH3 Abcam Cat#ab281584; RRID: AB_3697176 Anti-Ly6G Abcam Cat#ab25377; RRID: AB_470492 Anti-S100β Proteintech Cat#15146-1-AP; RRID: AB_2254244 Anti-Lcn2 Novus Cat#AF1857; RRID: AB_355022 Anti-CD31 Novus Cat#NB100-2284; RRID: AB_10002513 Anti-ZO-1 Proteintech Cat#21773-1-AP; RRID: AB_10733242 Anti-NeuN Sigma-Aldrich Cat#ABN90; RRID: AB_3696646 Anti-Ly6G BD Biosciences Cat#560599; RRID: AB_1727560 Alexa Fluor® 555 AffiniPureTM Donkey Anti-Rat IgG (H+L) Jackson ImmunoResearch Cat#712-565-150; RRID: AB_3095473 Alexa Fluor® 555 AffiniPureTM Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-565-150; RRID: AB_3095479 Alexa Fluor® 488 AffiniPureTM Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-545-150; RRID: AB_2340846 Alexa Fluor 488-conjugated AffiniPureTM Donkey Anti-Rabbit IgG Jackson ImmunoResearch Cat#711-545-152; RRID: AB_2313584 Donkey anti-Rabbit IgG (H+L) Secondary Antibody, Alexa FluorTM 555 Invitrogen Cat#A-31572; RRID: AB_162543 Donkey anti-Goat IgG (H+L) Secondary Antibody, Alexa FluorTM 594 Invitrogen Cat#A-11058; RRID: AB_2534105 Donkey anti-Goat IgG (H+L) Secondary Antibody, Alexa FluorTM Plus 488 Invitrogen Cat#A32814; RRID: AB_2762838 Alexa Fluor® 488 AffiniPureTM Donkey Anti-Chicken IgY (IgG) (H+L) Jackson ImmunoResearch Cat#703-545-155; RRID: AB_2340375 Alexa Fluor® 647 AffiniPureTM Donkey Anti-Chicken IgY (IgG) (H+L) Jackson ImmunoResearch Cat#703-605-155; RRID: AB_2340379 Bacterial and virus strains rAAV-GfaABC1D-GCaMP6f Braincase Cat#BC-0378 rAAV-Ef1α-DIO-hM3D(Gq)-mCherry Braincase Cat#BC-0146 rAAV-Ef1α-DIO-mCherry Braincase Cat#BC-0016 Biological samples Serum samples from patients Shanghai Yang Zhi Rehabilitation Hospital This paper Chemicals, peptides, and recombinant proteins Rose Bengal Sigma Cat#198250 Tamoxifen Sigma Cat#579000 DAPI Beyotime Cat#C1006 Fixable Viability Stain 510 BD Biosciences Cat#564406 Percoll Sigma Cat#P4937 PLX5622, AIN-6A SYSE Biotechnology Cat#D20010801 Phorbol myristate acetate Sigma Cat#524400 (Continued on next page) Neuron 113, 4199–4216.e1–e8, December 17, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Ionomycin Sigma Cat#I3909 Carprofen Sigma Cat#PHR1452 Dexamethasone MedChemExpress Cat#HY-14686 Enrofloxacin MedChemExpress Cat#HY-B0502 Pentobarbital sodium Sigma Cat#11715 Isoflurane Ruiwode Cat#R510-22-10 Evan’s blue Sigma Cat#E2129 Critical commercial assays RNAscopeTM Multiplex Fluorescent Reagent Kit v2 Advanced Cell Diagnostics Cat#323100 VECTASTAIN® Elite® ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 TSA Vivid Fluorophore 520 Advanced Cell Diagnostics Cat#PG-323271 TSA Vwid Fluorophore 650 Advanced Cell Diagnostics Cat#PG-323273 RNAscope Target RetrievalReagents Advanced Cell Diagnostics Cat#322000 RNAscope Probe Diluent Advanced Cell Diagnostics Cat#300041 Human MPO-DNA ELISA KIT jingkang Cat#JLC-Y4628 Human citH3-DNA ELISA KIT jingkang Cat#JLC87163 Mouse MPO-DNA ELISA KIT jingkang Cat#JLC87162 Mouse citH3-DNA ELISA KIT jingkang Cat#JLC87164 Experimental models: Organisms/strains C57BL/6 GemPharmatech Cat#N000013; RRID: IMSR_GPT: N000013 Lcn2 KO GemPharmatech Cat#T014584; RRID: IMSR_GPT: T014584 Lcn2loxP/loxP Shanghai Model Organisms Center Cat#NM-CKO-00134; RRID: IMSR_NM-CKO-00134 Ly6G-iCreERT2 Shanghai Model Organisms Center Cat#NM-KI-200218; RRID: IMSR_NM-KI-200218 Aldh1l1-CreERT2::Ai14 Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University This paper GFAP-iCreERT2 Jackson Laboratories Cat#012849; RRID: IMSR_JAK: 012849 RCL-GCaMP6s Jackson Laboratories Cat#028866; RRID: IMSR_JAX:028866 Pad4 KO Shanghai Model Organisms Center Cat#NM-KO-190334; RRID: IMSR_NM-KO-190334 Pad4-Flox/Ly6G-Cre-2A-tdTomato Shanghai Model Organisms Center Cat#NM-CKO-234151; RRID: IMSR_NM-CKO- 234151 Aldh1l1-Cre Jackson Laboratories Cat#023748; RRID: IMSR_JAX: 023748 Cx3cr1-GFP Jackson Laboratories Cat#005582; RRID: IMSR JAX: 005582 Oligonucleotides RNAscopeTM Probe- Mm-Padi4-C2 Advanced Cell Diagnostics Cat#467591-C2 RNAscopeTM Probe- Mm-Lcn2-C3 Advanced Cell Diagnostics Cat#313971-C3 Software and algorithms MATLAB R2014b Mathworks RRID: SCR_001622 FIJI ImageJ RRID: SCR_002285 Olympus FluoView Olympus RRID: SCR_014215 GraphPad Prism 8.0 GraphPad RRID: SCR_002798 IMARIS Oxford Instruments Group RRID: SCR_007274 Adobe Illustrator Adobe Systems RRID: SCR_010279 R (version 4.2.1) R Project https://www.r-project.org FlowJo software BD Biosciences RRID: SCR_000410 e2 Neuron 113, 4199–4216.e1–e8, December 17, 2025 ..
Software:Article Title: Selective removal of astrocytic PERK protects against glymphatic impairment and decreases toxic aggregation of β-amyloid and tau.
Article Snippet: Article Selective removal of astrocytic PERK protects against glymphatic impairment and decreases toxic aggregation of β-amyloid and tau Highlights • Astrocyte-specific PERK deletion restores protein synthesis and glymphatic function • Removal of astrocytic PERK reduces Aβ and tau aggregation • Cognitive performance is improved after astrocytic PERK deletion • Chronic PERK signaling disrupts perivascular AQP4 localization via CK2 Authors Kai Chen, Yosuke M. Morizawa, Tal Nuriel, Osama Al-Dalahmah, Zhongcong Xie, Guang Yang Correspondence zhongcong.Xie@uth.tmc.edu (Z.X.), gy2268@cumc.columbia.edu (G.Y.). In brief Chen et al. show that in AD mouse models, chronic activation of astrocytic PERK-eIF2a signaling suppresses protein synthesis and disrupts perivascular AQP4 localization via CK2- dependent mechanisms.. Inhibiting astrocytic PERK restores glymphatic function, reduces AD-related pathology, and improves cognitive performance.
Article Title: Lcn2 from neutrophil extracellular traps induces astrogliosis and post-stroke emotional disorders.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GFAP Millipore Cat#ab5541; RRID: AB_177521 Anti-Iba-1 Novus Biologicals Cat#nb100-1028; RRID: AB_3148646 Anti-MPO Proteintech Cat#66177-1-Ig; RRID: AB_2881572 Anti-citH3 Abcam Cat#ab281584; RRID: AB_3697176 Anti-Ly6G Abcam Cat#ab25377; RRID: AB_470492 Anti-S100β Proteintech Cat#15146-1-AP; RRID: AB_2254244 Anti-Lcn2 Novus Cat#AF1857; RRID: AB_355022 Anti-CD31 Novus Cat#NB100-2284; RRID: AB_10002513 Anti-ZO-1 Proteintech Cat#21773-1-AP; RRID: AB_10733242 Anti-NeuN Sigma-Aldrich Cat#ABN90; RRID: AB_3696646 Anti-Ly6G BD Biosciences Cat#560599; RRID: AB_1727560 Alexa Fluor® 555 AffiniPureTM Donkey Anti-Rat IgG (H+L) Jackson ImmunoResearch Cat#712-565-150; RRID: AB_3095473 Alexa Fluor® 555 AffiniPureTM Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-565-150; RRID: AB_3095479 Alexa Fluor® 488 AffiniPureTM Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-545-150; RRID: AB_2340846 Alexa Fluor 488-conjugated AffiniPureTM Donkey Anti-Rabbit IgG Jackson ImmunoResearch Cat#711-545-152; RRID: AB_2313584 Donkey anti-Rabbit IgG (H+L) Secondary Antibody, Alexa FluorTM 555 Invitrogen Cat#A-31572; RRID: AB_162543 Donkey anti-Goat IgG (H+L) Secondary Antibody, Alexa FluorTM 594 Invitrogen Cat#A-11058; RRID: AB_2534105 Donkey anti-Goat IgG (H+L) Secondary Antibody, Alexa FluorTM Plus 488 Invitrogen Cat#A32814; RRID: AB_2762838 Alexa Fluor® 488 AffiniPureTM Donkey Anti-Chicken IgY (IgG) (H+L) Jackson ImmunoResearch Cat#703-545-155; RRID: AB_2340375 Alexa Fluor® 647 AffiniPureTM Donkey Anti-Chicken IgY (IgG) (H+L) Jackson ImmunoResearch Cat#703-605-155; RRID: AB_2340379 Bacterial and virus strains rAAV-GfaABC1D-GCaMP6f Braincase Cat#BC-0378 rAAV-Ef1α-DIO-hM3D(Gq)-mCherry Braincase Cat#BC-0146 rAAV-Ef1α-DIO-mCherry Braincase Cat#BC-0016 Biological samples Serum samples from patients Shanghai Yang Zhi Rehabilitation Hospital This paper Chemicals, peptides, and recombinant proteins Rose Bengal Sigma Cat#198250 Tamoxifen Sigma Cat#579000 DAPI Beyotime Cat#C1006 Fixable Viability Stain 510 BD Biosciences Cat#564406 Percoll Sigma Cat#P4937 PLX5622, AIN-6A SYSE Biotechnology Cat#D20010801 Phorbol myristate acetate Sigma Cat#524400 (Continued on next page) Neuron 113, 4199–4216.e1–e8, December 17, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Ionomycin Sigma Cat#I3909 Carprofen Sigma Cat#PHR1452 Dexamethasone MedChemExpress Cat#HY-14686 Enrofloxacin MedChemExpress Cat#HY-B0502 Pentobarbital sodium Sigma Cat#11715 Isoflurane Ruiwode Cat#R510-22-10 Evan’s blue Sigma Cat#E2129 Critical commercial assays RNAscopeTM Multiplex Fluorescent Reagent Kit v2 Advanced Cell Diagnostics Cat#323100 VECTASTAIN® Elite® ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 TSA Vivid Fluorophore 520 Advanced Cell Diagnostics Cat#PG-323271 TSA Vwid Fluorophore 650 Advanced Cell Diagnostics Cat#PG-323273 RNAscope Target RetrievalReagents Advanced Cell Diagnostics Cat#322000 RNAscope Probe Diluent Advanced Cell Diagnostics Cat#300041 Human MPO-DNA ELISA KIT jingkang Cat#JLC-Y4628 Human citH3-DNA ELISA KIT jingkang Cat#JLC87163 Mouse MPO-DNA ELISA KIT jingkang Cat#JLC87162 Mouse citH3-DNA ELISA KIT jingkang Cat#JLC87164 Experimental models: Organisms/strains C57BL/6 GemPharmatech Cat#N000013; RRID: IMSR_GPT: N000013 Lcn2 KO GemPharmatech Cat#T014584; RRID: IMSR_GPT: T014584 Lcn2loxP/loxP Shanghai Model Organisms Center Cat#NM-CKO-00134; RRID: IMSR_NM-CKO-00134 Ly6G-iCreERT2 Shanghai Model Organisms Center Cat#NM-KI-200218; RRID: IMSR_NM-KI-200218 Aldh1l1-CreERT2::Ai14 Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University This paper GFAP-iCreERT2 Jackson Laboratories Cat#012849; RRID: IMSR_JAK: 012849 RCL-GCaMP6s Jackson Laboratories Cat#028866; RRID: IMSR_JAX:028866 Pad4 KO Shanghai Model Organisms Center Cat#NM-KO-190334; RRID: IMSR_NM-KO-190334 Pad4-Flox/Ly6G-Cre-2A-tdTomato Shanghai Model Organisms Center Cat#NM-CKO-234151; RRID: IMSR_NM-CKO- 234151 Aldh1l1-Cre Jackson Laboratories Cat#023748; RRID: IMSR_JAX: 023748 Cx3cr1-GFP Jackson Laboratories Cat#005582; RRID: IMSR JAX: 005582 Oligonucleotides RNAscopeTM Probe- Mm-Padi4-C2 Advanced Cell Diagnostics Cat#467591-C2 RNAscopeTM Probe- Mm-Lcn2-C3 Advanced Cell Diagnostics Cat#313971-C3 Software and algorithms MATLAB R2014b Mathworks RRID: SCR_001622 FIJI ImageJ RRID: SCR_002285 Olympus FluoView Olympus RRID: SCR_014215 GraphPad Prism 8.0 GraphPad RRID: SCR_002798 IMARIS Oxford Instruments Group RRID: SCR_007274 Adobe Illustrator Adobe Systems RRID: SCR_010279 R (version 4.2.1) R Project https://www.r-project.org FlowJo software BD Biosciences RRID: SCR_000410 e2 Neuron 113, 4199–4216.e1–e8, December 17, 2025 ..
Article Title: A brainstem to hypothalamic arcuate nucleus GABAergic circuit drives feeding.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit ani-c-Fos antibody Cell Signaling Cat#2250; RRID:AB_2247211 Rabbit anti-c-Fos antibody Merk Cat#ABE457; RRID:AB_2631318 Goat anti-mCherry antibody Scigen Cat#AB0040-200; RRID:AB_2333093 Rabbit anti-hrGFP antibody Agilent Cat#240141; RRID:AB_10596971 Rabitt anti-POMC antibody Phoenix Pharmaceuticals Cat#H-029-30; RRID:AB_2307442 Rabbit anti-RFP antibody Rockland Immunochemicals Cat#600-401-379; RRID:AB_2209751 Donkey anti-rabbit AlexaFluor 488 antibody Invitrogen Cat#A78948; RRID:AB_2921070 Donkey anti-chicken AlexaFluor 488 antibody Jackson immunoresearch Cat# 703-545-155; RRID:AB_2340375 Donkey anti-rabbit AlexaFluor 594 antibody Invitrogen Cat#A-21207; RRID:AB_141637 Donkey anti-goat AlexaFluor 594 antibody Invitrogen Cat#A-11058; RRID:AB_2534105 Donkey anti-goat Biotin-SP Jackson immunoresearch Cat# 711-065-152; RRID:AB_2340593 Bacterial and virus strains AAV8-hSyn-DIO-hM3D(Gq)-mCherry Addgene Cat#44361-AAV8; RRID:Addgene_44361 AAV8-hSyn-DIO-hM4D(Gi)-mCherry Addgene Cat#44362-AAV8; RRID:Addgene_44362 AAVrg-hSyn-fDIO-hM3D (Gq)-mCherry-WPREpA Addgene Cat#154868-AAVrg; RRID:Addgene_154868 AAV8-hSyn-DIO-mCherry Addgene Cat#50459-AAV8; RRID:Addgene_50459 AAV8-pEF1a-DIO-FLPo-WPRE-hGHpA Addgene Cat#87306-AAV8; RRID:Addgene_87306 AAV2-EF1a-DIO-ChR2 (E123T/T159C)-mCherry University of North Carolina Vector Core N/A AAV2-EF1a-DIO-ChR2 (E123T/T159C)-YFP University of North Carolina Vector Core N/A Chemicals, peptides, and recombinant proteins Clozapine-N-Oxide Tocris Cat#4936 Liraglutide Tocris Cat#6517 Ghrelin Tocris Cat#1463 Gabazine Tocris Cat#1262 GABA Tocris Cat#0344 CGP-55845 Tocris Cat#1248 MDL-72222 Tocris Cat#0640 QX-314 Tocris Cat#2313 ImmPACT DAB Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4105 VECTASTAIN ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-4000 Experimental models: Organisms/strains Mouse: Slc32a1tm2(cre)Lowl The Jackson Laboratory Cat#016962; RRID:IMSR_JAX:016962 Mouse: B6.FVB-Tg(Npy-hrGFP)1Lowl/J The Jackson Laboratory Cat#006417; RRID:IMSR_JAX:006417 Mouse: B6.Cg-Gt(ROSA)26Sortm9 (CAG-tdTomato)Hze/J The Jackson Laboratory Cat#007909; RRID:IMSR_JAX:007909 Mouse: Tg(Pomc-DsRed)18Low Prof. Malcom Low (University of Michigan) Hentges et al.75 Software and algorithms Prism 10 GraphPad Software https://www.graphpad.com/ RRID:SCR_002798 ImageJ NIH https://imagej.net/ij/RRID:SCR_003070 Affinity Designer 2 Serif https://affinity.serif.com/ (Continued on next page) e1 Current Biology 34, 1–11.e1–e4, April 22, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Arduino IDE Arduino https://www.arduino.cc/ RRID:SCR_024884 ANYmaze Stoelting https://www.any-maze.com/ RRID:SCR_014289 Phenomaster TSE-Systems https://www.tse-systems.com/ Axiovision Zen https://www.micro-shop.zeiss.com/ RRID:SCR_002677 RNAseq data Data are available from the NCBI Gene Expression Omnibus Accession GSE168737 Other 473-nm laser Laserglow Cat#LRS-0473 Optic fibers 200um, 0.39NA Thorlabs Cat#CFMLC Patch cables Thorlabs Cat#M83L1 Microinjector Narishige Cat#IM-11-2
RNAscope:Article Title: Lcn2 from neutrophil extracellular traps induces astrogliosis and post-stroke emotional disorders.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-GFAP Millipore Cat#ab5541; RRID: AB_177521 Anti-Iba-1 Novus Biologicals Cat#nb100-1028; RRID: AB_3148646 Anti-MPO Proteintech Cat#66177-1-Ig; RRID: AB_2881572 Anti-citH3 Abcam Cat#ab281584; RRID: AB_3697176 Anti-Ly6G Abcam Cat#ab25377; RRID: AB_470492 Anti-S100β Proteintech Cat#15146-1-AP; RRID: AB_2254244 Anti-Lcn2 Novus Cat#AF1857; RRID: AB_355022 Anti-CD31 Novus Cat#NB100-2284; RRID: AB_10002513 Anti-ZO-1 Proteintech Cat#21773-1-AP; RRID: AB_10733242 Anti-NeuN Sigma-Aldrich Cat#ABN90; RRID: AB_3696646 Anti-Ly6G BD Biosciences Cat#560599; RRID: AB_1727560 Alexa Fluor® 555 AffiniPureTM Donkey Anti-Rat IgG (H+L) Jackson ImmunoResearch Cat#712-565-150; RRID: AB_3095473 Alexa Fluor® 555 AffiniPureTM Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-565-150; RRID: AB_3095479 Alexa Fluor® 488 AffiniPureTM Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch Cat#715-545-150; RRID: AB_2340846 Alexa Fluor 488-conjugated AffiniPureTM Donkey Anti-Rabbit IgG Jackson ImmunoResearch Cat#711-545-152; RRID: AB_2313584 Donkey anti-Rabbit IgG (H+L) Secondary Antibody, Alexa FluorTM 555 Invitrogen Cat#A-31572; RRID: AB_162543 Donkey anti-Goat IgG (H+L) Secondary Antibody, Alexa FluorTM 594 Invitrogen Cat#A-11058; RRID: AB_2534105 Donkey anti-Goat IgG (H+L) Secondary Antibody, Alexa FluorTM Plus 488 Invitrogen Cat#A32814; RRID: AB_2762838 Alexa Fluor® 488 AffiniPureTM Donkey Anti-Chicken IgY (IgG) (H+L) Jackson ImmunoResearch Cat#703-545-155; RRID: AB_2340375 Alexa Fluor® 647 AffiniPureTM Donkey Anti-Chicken IgY (IgG) (H+L) Jackson ImmunoResearch Cat#703-605-155; RRID: AB_2340379 Bacterial and virus strains rAAV-GfaABC1D-GCaMP6f Braincase Cat#BC-0378 rAAV-Ef1α-DIO-hM3D(Gq)-mCherry Braincase Cat#BC-0146 rAAV-Ef1α-DIO-mCherry Braincase Cat#BC-0016 Biological samples Serum samples from patients Shanghai Yang Zhi Rehabilitation Hospital This paper Chemicals, peptides, and recombinant proteins Rose Bengal Sigma Cat#198250 Tamoxifen Sigma Cat#579000 DAPI Beyotime Cat#C1006 Fixable Viability Stain 510 BD Biosciences Cat#564406 Percoll Sigma Cat#P4937 PLX5622, AIN-6A SYSE Biotechnology Cat#D20010801 Phorbol myristate acetate Sigma Cat#524400 (Continued on next page) Neuron 113, 4199–4216.e1–e8, December 17, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Ionomycin Sigma Cat#I3909 Carprofen Sigma Cat#PHR1452 Dexamethasone MedChemExpress Cat#HY-14686 Enrofloxacin MedChemExpress Cat#HY-B0502 Pentobarbital sodium Sigma Cat#11715 Isoflurane Ruiwode Cat#R510-22-10 Evan’s blue Sigma Cat#E2129 Critical commercial assays RNAscopeTM Multiplex Fluorescent Reagent Kit v2 Advanced Cell Diagnostics Cat#323100 VECTASTAIN® Elite® ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 TSA Vivid Fluorophore 520 Advanced Cell Diagnostics Cat#PG-323271 TSA Vwid Fluorophore 650 Advanced Cell Diagnostics Cat#PG-323273 RNAscope Target RetrievalReagents Advanced Cell Diagnostics Cat#322000 RNAscope Probe Diluent Advanced Cell Diagnostics Cat#300041 Human MPO-DNA ELISA KIT jingkang Cat#JLC-Y4628 Human citH3-DNA ELISA KIT jingkang Cat#JLC87163 Mouse MPO-DNA ELISA KIT jingkang Cat#JLC87162 Mouse citH3-DNA ELISA KIT jingkang Cat#JLC87164 Experimental models: Organisms/strains C57BL/6 GemPharmatech Cat#N000013; RRID: IMSR_GPT: N000013 Lcn2 KO GemPharmatech Cat#T014584; RRID: IMSR_GPT: T014584 Lcn2loxP/loxP Shanghai Model Organisms Center Cat#NM-CKO-00134; RRID: IMSR_NM-CKO-00134 Ly6G-iCreERT2 Shanghai Model Organisms Center Cat#NM-KI-200218; RRID: IMSR_NM-KI-200218 Aldh1l1-CreERT2::Ai14 Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University This paper GFAP-iCreERT2 Jackson Laboratories Cat#012849; RRID: IMSR_JAK: 012849 RCL-GCaMP6s Jackson Laboratories Cat#028866; RRID: IMSR_JAX:028866 Pad4 KO Shanghai Model Organisms Center Cat#NM-KO-190334; RRID: IMSR_NM-KO-190334 Pad4-Flox/Ly6G-Cre-2A-tdTomato Shanghai Model Organisms Center Cat#NM-CKO-234151; RRID: IMSR_NM-CKO- 234151 Aldh1l1-Cre Jackson Laboratories Cat#023748; RRID: IMSR_JAX: 023748 Cx3cr1-GFP Jackson Laboratories Cat#005582; RRID: IMSR JAX: 005582 Oligonucleotides RNAscopeTM Probe- Mm-Padi4-C2 Advanced Cell Diagnostics Cat#467591-C2 RNAscopeTM Probe- Mm-Lcn2-C3 Advanced Cell Diagnostics Cat#313971-C3 Software and algorithms MATLAB R2014b Mathworks RRID: SCR_001622 FIJI ImageJ RRID: SCR_002285 Olympus FluoView Olympus RRID: SCR_014215 GraphPad Prism 8.0 GraphPad RRID: SCR_002798 IMARIS Oxford Instruments Group RRID: SCR_007274 Adobe Illustrator Adobe Systems RRID: SCR_010279 R (version 4.2.1) R Project https://www.r-project.org FlowJo software BD Biosciences RRID: SCR_000410 e2 Neuron 113, 4199–4216.e1–e8, December 17, 2025 ..
Protease Inhibitor:Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) e2 Immunity 57, 1–14.e1–e10, July 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) Immunity 57, 1–14.e1–e10, July 9, 2024 e3
Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) ll OPEN ACCESSArticle Immunity 57, 1696–1709.e1–e10, July 9, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) ll OPEN ACCESS Article e3 Immunity 57, 1696–1709.e1–e10, July 9, 2024
Western Blot:Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) e2 Immunity 57, 1–14.e1–e10, July 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) Immunity 57, 1–14.e1–e10, July 9, 2024 e3
Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) ll OPEN ACCESSArticle Immunity 57, 1696–1709.e1–e10, July 9, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) ll OPEN ACCESS Article e3 Immunity 57, 1696–1709.e1–e10, July 9, 2024
Staining:Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) e2 Immunity 57, 1–14.e1–e10, July 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) Immunity 57, 1–14.e1–e10, July 9, 2024 e3
Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) ll OPEN ACCESSArticle Immunity 57, 1696–1709.e1–e10, July 9, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) ll OPEN ACCESS Article e3 Immunity 57, 1696–1709.e1–e10, July 9, 2024
Single Cell:Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) e2 Immunity 57, 1–14.e1–e10, July 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) Immunity 57, 1–14.e1–e10, July 9, 2024 e3
Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) ll OPEN ACCESSArticle Immunity 57, 1696–1709.e1–e10, July 9, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) ll OPEN ACCESS Article e3 Immunity 57, 1696–1709.e1–e10, July 9, 2024
Avidin-Biotin Assay:Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) e2 Immunity 57, 1–14.e1–e10, July 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) Immunity 57, 1–14.e1–e10, July 9, 2024 e3
Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) ll OPEN ACCESSArticle Immunity 57, 1696–1709.e1–e10, July 9, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) ll OPEN ACCESS Article e3 Immunity 57, 1696–1709.e1–e10, July 9, 2024
Blocking Assay:Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) e2 Immunity 57, 1–14.e1–e10, July 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) Immunity 57, 1–14.e1–e10, July 9, 2024 e3
Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) ll OPEN ACCESSArticle Immunity 57, 1696–1709.e1–e10, July 9, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) ll OPEN ACCESS Article e3 Immunity 57, 1696–1709.e1–e10, July 9, 2024
Antibody Labeling:Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) e2 Immunity 57, 1–14.e1–e10, July 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) Immunity 57, 1–14.e1–e10, July 9, 2024 e3
Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) ll OPEN ACCESSArticle Immunity 57, 1696–1709.e1–e10, July 9, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) ll OPEN ACCESS Article e3 Immunity 57, 1696–1709.e1–e10, July 9, 2024
Reverse Transcription:Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) e2 Immunity 57, 1–14.e1–e10, July 9, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) Immunity 57, 1–14.e1–e10, July 9, 2024 e3
Article Title: The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER DPX Mountant for histology Sigma-Aldrich Cat#06522 Acrylamide Solution, Acryl-40 Amresco Cat#0132 Acrylamide Solution, Bis-2 Amresco Cat#0832 VA-044 Wako Cat#223-02112 Sodium azide Sigma-Aldrich Cat#71289 Streptavidin, Alexa Fluor 488 conjugate Life Technologies Cat#S11223 Hoechst 33342 Sigma-Aldrich Cat#B2261 TRI Reagent Sigma-Aldrich Cat#93289 Tris-EDTA buffer solution Sigma-Aldrich Cat#93302 RQ1 RNase-Free DNase Promega Cat#M6101 Fluorescein sodium salt Sigma-Aldrich Cat#166308 Evans blue Sigma-Aldrich Cat#E2129 Tissue-Tek O.C.T. .. Compound ProSciTech Cat#IA018 2-methylbutane Sigma-Aldrich Cat#320404 trichloroacetic Sigma-Aldrich Cat#91230 Protease Inhibitor Cocktail III Merck Millipore Cat#539134 Phosphatase Inhibitor Cocktail II Merck Millipore Cat#524625 Ponceau S solution Sigma-Aldrich Cat#P7170 Immobilon Western Chemiluminescent HRP Substrate Merck Millipore Cat#WBKLS0500 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat#L34961 RNeasy Micro Kit Qiagen Cat#74004 Mouse IFN-⍺ Miltenyi Biotech Cat#130-093-130 Chromium Single Cell 30 Library and Gel Bead Kit v3 10X Genomics Cat#1000075 VECTASTAIN Elite ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-6100 DAB Substrate Kit, Peroxidase (HRP), with Nickel Vector Laboratories Cat#SK-4100 Avidin/Biotin Blocking Kit Vector Laboratories Cat#SP-2001 Vector NovaRED Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4800 Mix-n-Stain CF 647 Antibody Labeling Kit Sigma-Aldrich Cat#MX647S50 Mix-n-Stain CF 568 Antibody Labeling Kit Sigma-Aldrich Cat#MA568S50 BSA Removal Kit Abcam Cat#ab173231 RevertAid RT Reverse Transcription Kit Thermo Fisher Scientific Cat#K1691 SensiFAST SYBR Lo-ROX Kit Bioline Cat#BIO-94020 Pierce BCA Protein Assay Kit Thermo Fisher Scientific Cat#23225 Minimum Essential Medium Eagle Sigma-Aldrich Cat#M2279 HEPES solution Sigma-Aldrich Cat#H0887 Papain from papaya latex Sigma-Aldrich Cat#P3125 L-cysteine Sigma-Aldrich Cat#C7352 Deoxyribonuclease I from bovine pancreas Sigma-Aldrich Cat#D5025 Fetal Bovine Serum Sigma-Aldrich Cat#12003C Penicillin-Streptomycin (10,000 U/mL) Thermo Fisher Scientific Cat#15140163 Poly-D-Lysine solution Merck Millipore Cat#A-003-E Adult Brain Dissociation Kit Miltenyi Biotec Cat#130-107-677 Ammonium Chloride Solution Stemcell Technologies Cat#07850 Critical commercial assays Quanterix Homebrew Simoa Kit Quanterix Cat#101354 Mouse Interferon alpha 1 ELISA Kit Abcam Cat#ab252352 (Continued on next page) ll OPEN ACCESSArticle Immunity 57, 1696–1709.e1–e10, July 9, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data scRNASeq data This paper ENA: PRJEB44230 Experimental models: Organisms/strains Mouse: GIFN mice (B6;C-Tg(Gfap-Ifna1)39Ilc/Niusy) Akwa et al.14; Campbell et al.15 RRID:MGI:7328531 Mouse: IFNAR1 floxed (Ifnar1tm1Uka) Dr Peter Crack (University of Melbourne) MGI:2655303 Mouse: Tek-Cre (B6.Cg-Tg(Tek-cre)12Flv/J) The Jackson Laboratory RRID:IMSR_JAX:004128 Mouse: Cx3cr1-Cre (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) The Jackson Laboratory RRID:IMSR_JAX:025524 Mouse: C57BL/6J Australian BioResource C57BL/6JAusb Oligonucleotides See Table S5 N/A Software and algorithms Fiji NIH https://fiji.sc/; RRID:SCR_002285 Cell Ranger v3.0.2, v3.1.0 10X Genomics https://www.10xgenomics.com/support/ software/cell-ranger/downloads/; RRID:SCR_017344 Loupe Browser v4 10X Genomics https://www.10xgenomics.com/support/ software/loupe-browser/downloads; RRID:SCR_018555 R v3.6.1, v4.0.2 R https://www.r-project.org/; RRID: SCR_002394 gplots v3.1.0 Warnes et al.34 https://cran.r-project.org/web/ packages/gplots/ ggplot2 v3.3.2 Wickham35 https://cran.r-project.org/web/ packages/ggplot2/index.html Panther v18.0 Mi and Thomas36; Thomas et al.37 https://pantherdb.org/; RRID:SCR_004869 SPOT Advanced 4.5 Spot Imaging http://www.spotimaging.com/software/ spot-advanced/; RRID:SCR_016613 Imaris v9 Oxford Instruments http://www.bitplane.com/imaris/ imaris; RRID:SCR_007370 TreadScan CleverSys https://cleversysinc.com/CleverSysInc/ csi_products/treadscan/ GraphPad Prism v8 and v9 GraphPad Software http://www.graphpad.com/; RRID:SCR_002798 survminer v0.4.6 Kassambara et al.38 https://CRAN.R-project.org/ package=survminer; RRID:SCR_021094 ordinal v2019.12-10 Christensen39 https://CRAN.R-project.org/ package=ordinal; RRID:SCR_022856 lme4 v1.1-21 Bates et al.40 https://CRAN.R-project.org/ package=lme4; RRID:SCR_015654 emmeans v1.4.3 Lenth et al.41 https://CRAN.R-project.org/ package=emmeans; RRID:SCR_018734 FlowJo v10 BD Biosciences https://www.flowjo.com/solutions/ flowjo; RRID:SCR_008520 Other UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-41 Latex beads, carboxylate-modified polystyrene, fluorescent yellow-green Sigma-Aldrich Cat#L4655 (Continued on next page) ll OPEN ACCESS Article e3 Immunity 57, 1696–1709.e1–e10, July 9, 2024
Virus:Article Title: A brainstem to hypothalamic arcuate nucleus GABAergic circuit drives feeding.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit ani-c-Fos antibody Cell Signaling Cat#2250; RRID:AB_2247211 Rabbit anti-c-Fos antibody Merk Cat#ABE457; RRID:AB_2631318 Goat anti-mCherry antibody Scigen Cat#AB0040-200; RRID:AB_2333093 Rabbit anti-hrGFP antibody Agilent Cat#240141; RRID:AB_10596971 Rabitt anti-POMC antibody Phoenix Pharmaceuticals Cat#H-029-30; RRID:AB_2307442 Rabbit anti-RFP antibody Rockland Immunochemicals Cat#600-401-379; RRID:AB_2209751 Donkey anti-rabbit AlexaFluor 488 antibody Invitrogen Cat#A78948; RRID:AB_2921070 Donkey anti-chicken AlexaFluor 488 antibody Jackson immunoresearch Cat# 703-545-155; RRID:AB_2340375 Donkey anti-rabbit AlexaFluor 594 antibody Invitrogen Cat#A-21207; RRID:AB_141637 Donkey anti-goat AlexaFluor 594 antibody Invitrogen Cat#A-11058; RRID:AB_2534105 Donkey anti-goat Biotin-SP Jackson immunoresearch Cat# 711-065-152; RRID:AB_2340593 Bacterial and virus strains AAV8-hSyn-DIO-hM3D(Gq)-mCherry Addgene Cat#44361-AAV8; RRID:Addgene_44361 AAV8-hSyn-DIO-hM4D(Gi)-mCherry Addgene Cat#44362-AAV8; RRID:Addgene_44362 AAVrg-hSyn-fDIO-hM3D (Gq)-mCherry-WPREpA Addgene Cat#154868-AAVrg; RRID:Addgene_154868 AAV8-hSyn-DIO-mCherry Addgene Cat#50459-AAV8; RRID:Addgene_50459 AAV8-pEF1a-DIO-FLPo-WPRE-hGHpA Addgene Cat#87306-AAV8; RRID:Addgene_87306 AAV2-EF1a-DIO-ChR2 (E123T/T159C)-mCherry University of North Carolina Vector Core N/A AAV2-EF1a-DIO-ChR2 (E123T/T159C)-YFP University of North Carolina Vector Core N/A Chemicals, peptides, and recombinant proteins Clozapine-N-Oxide Tocris Cat#4936 Liraglutide Tocris Cat#6517 Ghrelin Tocris Cat#1463 Gabazine Tocris Cat#1262 GABA Tocris Cat#0344 CGP-55845 Tocris Cat#1248 MDL-72222 Tocris Cat#0640 QX-314 Tocris Cat#2313 ImmPACT DAB Substrate Kit, Peroxidase Vector Laboratories Cat#SK-4105 VECTASTAIN ABC-HRP Kit, Peroxidase (Standard) Vector Laboratories CatPK-4000 Experimental models: Organisms/strains Mouse: Slc32a1tm2(cre)Lowl The Jackson Laboratory Cat#016962; RRID:IMSR_JAX:016962 Mouse: B6.FVB-Tg(Npy-hrGFP)1Lowl/J The Jackson Laboratory Cat#006417; RRID:IMSR_JAX:006417 Mouse: B6.Cg-Gt(ROSA)26Sortm9 (CAG-tdTomato)Hze/J The Jackson Laboratory Cat#007909; RRID:IMSR_JAX:007909 Mouse: Tg(Pomc-DsRed)18Low Prof. Malcom Low (University of Michigan) Hentges et al.75 Software and algorithms Prism 10 GraphPad Software https://www.graphpad.com/ RRID:SCR_002798 ImageJ NIH https://imagej.net/ij/RRID:SCR_003070 Affinity Designer 2 Serif https://affinity.serif.com/ (Continued on next page) e1 Current Biology 34, 1–11.e1–e4, April 22, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Arduino IDE Arduino https://www.arduino.cc/ RRID:SCR_024884 ANYmaze Stoelting https://www.any-maze.com/ RRID:SCR_014289 Phenomaster TSE-Systems https://www.tse-systems.com/ Axiovision Zen https://www.micro-shop.zeiss.com/ RRID:SCR_002677 RNAseq data Data are available from the NCBI Gene Expression Omnibus Accession GSE168737 Other 473-nm laser Laserglow Cat#LRS-0473 Optic fibers 200um, 0.39NA Thorlabs Cat#CFMLC Patch cables Thorlabs Cat#M83L1 Microinjector Narishige Cat#IM-11-2
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