Virus:Article Title: Stress-induced TDP-43 nuclear condensation causes splicing loss of function and STMN2 depletion.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse Monoclonal anti-TDP-43 R&D Biosystems Cat# MAB77781 Rabbit Polyclonal anti-TDP-43 C-terminal Sigma Cat# T1580 Rabbit Monoclonal anti-TDP-43 (E2G6G) Cell Signaling Cat# 89718 Rabbit Polyclonal anti-Flag tag (DYKDDDDK) Proteintech Cat# 20543-1-AP Rabbit Polyclonal anti-pinin/PNN Proteintech Cat# 18266-1-AP Mouse Monoclonal anti-coilin/p80 BD Biosciences Cat# 612074 Rabbit Polyclonal anti-PML Proteintech Cat# 21041-1-AP Rabbit Polyclonal anti-SAFB Proteintech Cat# 21857-1-AP Rabbit Polyclonal anti-GFP Proteintech Cat# 50430-2-AP Rabbit Polyclonal anti-STMN2 Proteintech Cat# 10586-1-AP Mouse Monoclonal anti-STMN2 Biotechne Cat# MAB6930 Mouse Monoclonal anti-GFP Proteintech Cat# 66002-1-Ig Rabbit Polyclonal anti-NONO Proteintech Cat# 11058-1-AP Rabbit Polyclonal anti-YBX1 Proteintech Cat# 20339-1-AP Rabbit Polyclonal anti-hnRNPC Proteintech Cat# 11760-1-AP Mouse Monoclonal anti-NPM1 Proteintech Cat# 60096-1-Ig Rabbit Polyclonal anti-A11 oligomer ThermoFisher Cat# AHB0052 Rabbit Polyclonal anti-GAPDH Proteintech Cat# 10494-1-A Biotinylated goat anti-rabbit IgG Vector labs Cat# BA-1000 Mouse IgG HRP Linked Whole Ab Amersham Cat# NA931 Rabbit IgG HRP Linked Whole Ab Amersham Cat# NA934 Secondary fluorescently-labeled antibodies: Alexa 488/546 Fluor anti-mouse/rabbit IgG ThermoFisher Cat# A-11008; A-11001; A-11030; A-11035 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) New England Biolabs Cat# C3040H NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat# C2987H Biological samples Human postmortem tissue (spinal cord) London Neurodegenerative Diseases Brain Bank request #1470 Chemicals, peptides, and recombinant proteins Actinomycin D Sigma-Aldrich Cat#A1410 Pladienolide B Cayman Chemicals Cat#16538 Urea Sigma-Aldrich Cat#U5128 SSC, 203 concentrate Sigma-Aldrich Cat#SRE0068 Formamide Sigma-Aldrich Cat#F9037 RNase A New England Biolabs Cat#T3018L MG132 Sigma-Aldrich Cat#M7449 Polyinosinic-polycytidylic acid Sigma-Aldrich Cat#P9582 NaAsO2 Sigma-Aldrich Cat#S7400 1,6-hexanediol Sigma-Aldrich Cat#240117 Oligomycin A Sigma-Aldrich Cat#75351 2-deoxy-glucose ApexBio Cat#B1027 Polyinosinic-polycytidylic acid potassium salt, poly(I:C) Sigma-Aldrich Cat#P9582 (Continued on next page) 16 Cell Reports 43, 114421, July 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Cycloheximide Sigma-Aldrich Cat#C7698 Poly-L-Lysine Sigma-Aldrich Cat#25988-63-0 Aqueous Glutaraldehyde EM Grade EMS Diasum Cat#16110 Bovine Serum Albumin (BSA) Jackson ImmunoResearch Cat#001-000-161 Disuccinimidyl glutarate (DSG) Sigma-Aldrich Cat#80424 Recombinant TDP-43 R&D Biosystems Cat#AP-190-100 Critical commercial assays Herculase II Fusion DNA polymerase Agilent Cat#600675 Zero BluntTM TOPOTM kit ThermoFisher Cat#450245 Lipofectamine2000 Transfection Reagent ThermoFisher Cat#11668027 M-MLV Reverse Transcriptase Promega Cat#M1701 qPCRBIO SyGreen Mix Lo-Rox PCR Biosystems Cat#PB20.11–05 GoTaq Green Master Mix Promega Cat#M712 JetPRIME Transfection Reagent PolyPlus Cat#101000027 GenEluteTM Mammalian Total RNA Miniprep Kit Sigma-Aldrich Cat#RTN350 QIAzol Lysis Reagent Qiagen Cat#79306 Chromotek GFP-Trap agarose Proteintech Cat#gta STEMdiffTM Astrocyte Differentiation Kit Stemcell Technologies Cat#100-0013 RiboLock RNase inhibitor ThermoFisher Cat#EO0381 Vectastain ABC reagent Kit Vector Labs Cat#PK6100 ImPACT DAB reagent Kit Vector Labs Cat#SK-4103 RNase free DNase set Qiagen Cat#79254 Ni-NTA Superflow beads Qiagen Cat#30410 His-streptavidin NKMAX Cat#stv0801 cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Roche Cat#4693132001 10% Mini-PROTEAN TGXTM Precast Gel, 15-well Bio-Rad Cat#4561036 Clarity Max Western ECL Substrate Bio-Rad Cat#1705062 GelCodeTM Blue Safe Protein Stain ThermoFisher Cat#24594 EprediaTM Immu-MountTM ThermoFisher Cat#10622689 Deposited data Raw and processed proteomics data for: 1) TC proteome; 2) soluble nuclear TDP-43 interactome jPOST partner repository (https://jpostdb.org) JPST003167 (PXD052963) Experimental models: Cell lines Human: HeLa cells (ATCC) Sigma-Aldrich Cat#93021013 Human: SH-SY5Y neuroblastoma cells (ATCC) Sigma-Aldrich Cat#94030304 Human: neural precursors (Day 16), motor neurons (Day 42) and astrocytes derived from ES H9 line Shelkovnikova et al.23 and this paper N/A Oligonucleotides Silencer Select : TARDBP (s23829) ThermoFisher Cat#4392420 AllStars Negative Control siRNA Qiagen Cat#SI03650318 Oligo(dT)30-Cy5 DNA FISH probe Sigma N/A Random hexamers ThermoFisher Cat#48190011 Primers for RT-qPCR and PCR, see Table S2 An et al.85; Cao et al.50; this paper N/A (Continued on next page) Cell Reports 43, 114421, July 23, 2024 17
Recombinant:Article Title: Stress-induced TDP-43 nuclear condensation causes splicing loss of function and STMN2 depletion.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse Monoclonal anti-TDP-43 R&D Biosystems Cat# MAB77781 Rabbit Polyclonal anti-TDP-43 C-terminal Sigma Cat# T1580 Rabbit Monoclonal anti-TDP-43 (E2G6G) Cell Signaling Cat# 89718 Rabbit Polyclonal anti-Flag tag (DYKDDDDK) Proteintech Cat# 20543-1-AP Rabbit Polyclonal anti-pinin/PNN Proteintech Cat# 18266-1-AP Mouse Monoclonal anti-coilin/p80 BD Biosciences Cat# 612074 Rabbit Polyclonal anti-PML Proteintech Cat# 21041-1-AP Rabbit Polyclonal anti-SAFB Proteintech Cat# 21857-1-AP Rabbit Polyclonal anti-GFP Proteintech Cat# 50430-2-AP Rabbit Polyclonal anti-STMN2 Proteintech Cat# 10586-1-AP Mouse Monoclonal anti-STMN2 Biotechne Cat# MAB6930 Mouse Monoclonal anti-GFP Proteintech Cat# 66002-1-Ig Rabbit Polyclonal anti-NONO Proteintech Cat# 11058-1-AP Rabbit Polyclonal anti-YBX1 Proteintech Cat# 20339-1-AP Rabbit Polyclonal anti-hnRNPC Proteintech Cat# 11760-1-AP Mouse Monoclonal anti-NPM1 Proteintech Cat# 60096-1-Ig Rabbit Polyclonal anti-A11 oligomer ThermoFisher Cat# AHB0052 Rabbit Polyclonal anti-GAPDH Proteintech Cat# 10494-1-A Biotinylated goat anti-rabbit IgG Vector labs Cat# BA-1000 Mouse IgG HRP Linked Whole Ab Amersham Cat# NA931 Rabbit IgG HRP Linked Whole Ab Amersham Cat# NA934 Secondary fluorescently-labeled antibodies: Alexa 488/546 Fluor anti-mouse/rabbit IgG ThermoFisher Cat# A-11008; A-11001; A-11030; A-11035 Bacterial and virus strains NEB Stable Competent E. coli (High Efficiency) New England Biolabs Cat# C3040H NEB 5-alpha Competent E. coli (High Efficiency) New England Biolabs Cat# C2987H Biological samples Human postmortem tissue (spinal cord) London Neurodegenerative Diseases Brain Bank request #1470 Chemicals, peptides, and recombinant proteins Actinomycin D Sigma-Aldrich Cat#A1410 Pladienolide B Cayman Chemicals Cat#16538 Urea Sigma-Aldrich Cat#U5128 SSC, 203 concentrate Sigma-Aldrich Cat#SRE0068 Formamide Sigma-Aldrich Cat#F9037 RNase A New England Biolabs Cat#T3018L MG132 Sigma-Aldrich Cat#M7449 Polyinosinic-polycytidylic acid Sigma-Aldrich Cat#P9582 NaAsO2 Sigma-Aldrich Cat#S7400 1,6-hexanediol Sigma-Aldrich Cat#240117 Oligomycin A Sigma-Aldrich Cat#75351 2-deoxy-glucose ApexBio Cat#B1027 Polyinosinic-polycytidylic acid potassium salt, poly(I:C) Sigma-Aldrich Cat#P9582 (Continued on next page) 16 Cell Reports 43, 114421, July 23, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Cycloheximide Sigma-Aldrich Cat#C7698 Poly-L-Lysine Sigma-Aldrich Cat#25988-63-0 Aqueous Glutaraldehyde EM Grade EMS Diasum Cat#16110 Bovine Serum Albumin (BSA) Jackson ImmunoResearch Cat#001-000-161 Disuccinimidyl glutarate (DSG) Sigma-Aldrich Cat#80424 Recombinant TDP-43 R&D Biosystems Cat#AP-190-100 Critical commercial assays Herculase II Fusion DNA polymerase Agilent Cat#600675 Zero BluntTM TOPOTM kit ThermoFisher Cat#450245 Lipofectamine2000 Transfection Reagent ThermoFisher Cat#11668027 M-MLV Reverse Transcriptase Promega Cat#M1701 qPCRBIO SyGreen Mix Lo-Rox PCR Biosystems Cat#PB20.11–05 GoTaq Green Master Mix Promega Cat#M712 JetPRIME Transfection Reagent PolyPlus Cat#101000027 GenEluteTM Mammalian Total RNA Miniprep Kit Sigma-Aldrich Cat#RTN350 QIAzol Lysis Reagent Qiagen Cat#79306 Chromotek GFP-Trap agarose Proteintech Cat#gta STEMdiffTM Astrocyte Differentiation Kit Stemcell Technologies Cat#100-0013 RiboLock RNase inhibitor ThermoFisher Cat#EO0381 Vectastain ABC reagent Kit Vector Labs Cat#PK6100 ImPACT DAB reagent Kit Vector Labs Cat#SK-4103 RNase free DNase set Qiagen Cat#79254 Ni-NTA Superflow beads Qiagen Cat#30410 His-streptavidin NKMAX Cat#stv0801 cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Roche Cat#4693132001 10% Mini-PROTEAN TGXTM Precast Gel, 15-well Bio-Rad Cat#4561036 Clarity Max Western ECL Substrate Bio-Rad Cat#1705062 GelCodeTM Blue Safe Protein Stain ThermoFisher Cat#24594 EprediaTM Immu-MountTM ThermoFisher Cat#10622689 Deposited data Raw and processed proteomics data for: 1) TC proteome; 2) soluble nuclear TDP-43 interactome jPOST partner repository (https://jpostdb.org) JPST003167 (PXD052963) Experimental models: Cell lines Human: HeLa cells (ATCC) Sigma-Aldrich Cat#93021013 Human: SH-SY5Y neuroblastoma cells (ATCC) Sigma-Aldrich Cat#94030304 Human: neural precursors (Day 16), motor neurons (Day 42) and astrocytes derived from ES H9 line Shelkovnikova et al.23 and this paper N/A Oligonucleotides Silencer Select : TARDBP (s23829) ThermoFisher Cat#4392420 AllStars Negative Control siRNA Qiagen Cat#SI03650318 Oligo(dT)30-Cy5 DNA FISH probe Sigma N/A Random hexamers ThermoFisher Cat#48190011 Primers for RT-qPCR and PCR, see Table S2 An et al.85; Cao et al.50; this paper N/A (Continued on next page) Cell Reports 43, 114421, July 23, 2024 17
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