Derivative Assay:Article Title: Salmonella Typhimurium effector SseI regulates host peroxisomal dynamics to acquire lysosomal cholesterol.
Article Snippet: .. Reagents and tools table Reagent/Resource Reference or Source Identifier or Catalog Number Experimental models HeLa cells (H. sapiens) ATCC CCL-2 LOT: 70056809 Monocytes derived macrophages (H. sapiens) Blood bank at the Transfusion Medicine - King Georges’ Medical University Salmonella Typhimurium Kind gift from Prof. Michael Hensel ATCC, 14028 C57BL6/J (M. musculus) Central Animal Facility, IISc Bangalore, India. .. Recombinant DNA pLJC5-3XMyc-EGFP-PEX26 Addgene 139059 pcDNA3 flag HA: SseI This study Vector backbone from #9021, Addgene pcDNA3 flag HA: ARF1 This study Vector backbone from #9021, Addgene pFPV-mCherry Addgene 20956 pET23A His tagged SseI This study N/A pQE60 myc::sseI This study N/A pQE60 sseI::myc This study N/A SseI, Syt7, and ARF1 (along with mutants) were synthesized commercially GenScript Antibodies Rabbit Anti-LAMP1 Cell Signalling Technology (CST) D401S Anti-FLAG CST 8146 Anti-myc CST 2276 Anti-Pex14 ABclonal A7336 Anti-ESYT1 ABclonal A15410 Anti-ABCD1 Proteintech 60153-1-Ig Anti-pex5 Proteintech 12545-1-AP Anti-ARF1 Proteintech 10790-1-AP Anti-GAPDH Invitrogen T0004 Anti-HA CiteAb 2367 Anti-SYT7 Novus Biologicals NBP2-22420 PIP2 antibody Novus Biologicals NBP2-76433 Goat anti-mouse IgG Alexa fluor 594 CiteAb A-11032 Goat anti-Rabbit IgG Alexa Fluor 488 CiteAb A-11034 Goat anti-rabbit IgG Cy5 Invitrogen A10523 Control Mouse immunoglobulin Invitrogen 500-M00-1MG Control rabbit immunoglobulin PeproTech 500-P00-500μg horseradish peroxidase CST 7074P2 Oligonucleotides and other sequence-based reagents ARF1 Santa Cruz SC-105086 Synaptotagmin VII (SYT7) Santa Cruz SC-41320 E-Syt1 Santa Cruz SC-95714 16 EMBO reports © The Author(s) D ow nloaded from https://w w w .em bopress.org on D ecem ber 25, 2024 from IP 2402:800:6343:b0f8:400f:1124:9738:8c7d.
other:
Recombinant:Article Title: RudLOV is an optically synchronized cargo transport method revealing unexpected effects of dynasore.
Article Snippet: .. Reagents and tools table Reagent/Resource Reference or Source Identifier or Catalog Number Experimental models HeLa cells (H. sapiens) ATCC CCL-2 Recombinant DNA CMV-ManII-EGFP This work CMV-2xCv-GM130 This work CMV-2xRb-GM130 This work CMV-TfR-2xSca This work pEGFP VAMP3 Addgene 42310 CT7-2xSca-Rab6a This work CT7-2xNG-COPe This work pEBP-Sec61b-mTagBFP2LL-LOV2 This work CMV-SP-Zdk-2xCv-GPI This work CMV-SP-Zdk-2xCvVSVG This work CMV-SP-Zdk-2xScaVSVG This work Reagent/Resource Reference or Source Identifier or Catalog Number CMV-TNF-Zdk-2xCv This work CMV-TNF-Zdk-2xSca This work Str-KDEL_SBP-2xSca-GPI This work Str-KDEL_SBP-2NGVSVG This work Chemicals, Enzymes and other reagents D-MEM(High Glucose) FUJIFILM Wako Chemicals 045-30285 Penicillin-StreptomycinL-Glutamine Solution (×100) FUJIFILM Wako Chemicals 161-23201 100mmol/L Sodium Pyruvate FUJIFILM Wako Chemicals 190-14881 1 mol/l-HEPES Buffer Nacalai Tesque 17557-94 Fetal Bovine Serum Nichirei 174012 Dynasore Cayman Chemicals 14062 Nocodazole Cayman Chemicals 13857 Cycloheximide Cayman Chemicals 14126 Dynole 34-2 Abcam 120464 Dynole 31-2 Abcam 120474 Dyngo-4a Cayman Chemicals 29479 Biotin FUJIFILM Wako Chemicals 029-08713 Biliverdine TRC B386400 ibidi® μ-Slide 8-well ibidi 80826 JetPrime Polyplus 101000015 JetOptimus Polyplus 101000006 G418 sulfate FUJIFILM Wako Chemicals 078-05961 Puromycin Dihydrochloride FUJIFILM Wako Chemicals 160-23151 2% uranyl acetate Electron Microscopy Sciences 22400-2 8% glutaraldehyde Electron Microscopy Sciences 16000 16% paraformaldehyde Electron Microscopy Sciences 15700 4% osmium tetroxide Electron Microscopy Sciences 19100 EPON-812 Electron Microscopy Sciences 14900 Aclar-film Nisshin-EM 453 Soium cacodylate FUJIFILM Wako Chemicals 194-04852 DAB(3,3’Diaminobenzidine Tetrahydrochloride) FUJIFILM Wako Chemicals 349-00903 Hydrogen Peroxide FUJIFILM Wako Chemicals 081-04215 Software Fiji/ImageJ https://imagej.net/software/ fiji/ Volocity https://www.volocity4d.com Other FV3000 https://www.olympuslifescience.com/ja/laserscanning/fv3000/ SCLIM Kurokawa et al, 2013 10 EMBO reports © The Author(s) D ow nloaded from https://w w w .em bopress.org on D ecem ber 12, 2024 from IP 27.34.65.10. .. Reagent/Resource Reference or Source Identifier or Catalog Number Ultramicrotome EM UC7 Leica SEM Regulus8240 Hitachi TEM JEM1400 JEOL Construction of plasmids for RudLOV and organelle markers The fluorescent tags described herein, Clover, Ruby, NeonGreen, and Scarlet, are tandem repeats of two identical fluorescent proteins, mClover3, mRuby3 (gift from Michael Lin; (Bajar et al, 2016), and mNeonGreen and mScarlet-I (gift from Erik Dent; (Taylor et al, 2020), respectively.
Electron Microscopy:Article Title: RudLOV is an optically synchronized cargo transport method revealing unexpected effects of dynasore.
Article Snippet: .. Reagents and tools table Reagent/Resource Reference or Source Identifier or Catalog Number Experimental models HeLa cells (H. sapiens) ATCC CCL-2 Recombinant DNA CMV-ManII-EGFP This work CMV-2xCv-GM130 This work CMV-2xRb-GM130 This work CMV-TfR-2xSca This work pEGFP VAMP3 Addgene 42310 CT7-2xSca-Rab6a This work CT7-2xNG-COPe This work pEBP-Sec61b-mTagBFP2LL-LOV2 This work CMV-SP-Zdk-2xCv-GPI This work CMV-SP-Zdk-2xCvVSVG This work CMV-SP-Zdk-2xScaVSVG This work Reagent/Resource Reference or Source Identifier or Catalog Number CMV-TNF-Zdk-2xCv This work CMV-TNF-Zdk-2xSca This work Str-KDEL_SBP-2xSca-GPI This work Str-KDEL_SBP-2NGVSVG This work Chemicals, Enzymes and other reagents D-MEM(High Glucose) FUJIFILM Wako Chemicals 045-30285 Penicillin-StreptomycinL-Glutamine Solution (×100) FUJIFILM Wako Chemicals 161-23201 100mmol/L Sodium Pyruvate FUJIFILM Wako Chemicals 190-14881 1 mol/l-HEPES Buffer Nacalai Tesque 17557-94 Fetal Bovine Serum Nichirei 174012 Dynasore Cayman Chemicals 14062 Nocodazole Cayman Chemicals 13857 Cycloheximide Cayman Chemicals 14126 Dynole 34-2 Abcam 120464 Dynole 31-2 Abcam 120474 Dyngo-4a Cayman Chemicals 29479 Biotin FUJIFILM Wako Chemicals 029-08713 Biliverdine TRC B386400 ibidi® μ-Slide 8-well ibidi 80826 JetPrime Polyplus 101000015 JetOptimus Polyplus 101000006 G418 sulfate FUJIFILM Wako Chemicals 078-05961 Puromycin Dihydrochloride FUJIFILM Wako Chemicals 160-23151 2% uranyl acetate Electron Microscopy Sciences 22400-2 8% glutaraldehyde Electron Microscopy Sciences 16000 16% paraformaldehyde Electron Microscopy Sciences 15700 4% osmium tetroxide Electron Microscopy Sciences 19100 EPON-812 Electron Microscopy Sciences 14900 Aclar-film Nisshin-EM 453 Soium cacodylate FUJIFILM Wako Chemicals 194-04852 DAB(3,3’Diaminobenzidine Tetrahydrochloride) FUJIFILM Wako Chemicals 349-00903 Hydrogen Peroxide FUJIFILM Wako Chemicals 081-04215 Software Fiji/ImageJ https://imagej.net/software/ fiji/ Volocity https://www.volocity4d.com Other FV3000 https://www.olympuslifescience.com/ja/laserscanning/fv3000/ SCLIM Kurokawa et al, 2013 10 EMBO reports © The Author(s) D ow nloaded from https://w w w .em bopress.org on D ecem ber 12, 2024 from IP 27.34.65.10. .. Reagent/Resource Reference or Source Identifier or Catalog Number Ultramicrotome EM UC7 Leica SEM Regulus8240 Hitachi TEM JEM1400 JEOL Construction of plasmids for RudLOV and organelle markers The fluorescent tags described herein, Clover, Ruby, NeonGreen, and Scarlet, are tandem repeats of two identical fluorescent proteins, mClover3, mRuby3 (gift from Michael Lin; (Bajar et al, 2016), and mNeonGreen and mScarlet-I (gift from Erik Dent; (Taylor et al, 2020), respectively.
Software:Article Title: RudLOV is an optically synchronized cargo transport method revealing unexpected effects of dynasore.
Article Snippet: .. Reagents and tools table Reagent/Resource Reference or Source Identifier or Catalog Number Experimental models HeLa cells (H. sapiens) ATCC CCL-2 Recombinant DNA CMV-ManII-EGFP This work CMV-2xCv-GM130 This work CMV-2xRb-GM130 This work CMV-TfR-2xSca This work pEGFP VAMP3 Addgene 42310 CT7-2xSca-Rab6a This work CT7-2xNG-COPe This work pEBP-Sec61b-mTagBFP2LL-LOV2 This work CMV-SP-Zdk-2xCv-GPI This work CMV-SP-Zdk-2xCvVSVG This work CMV-SP-Zdk-2xScaVSVG This work Reagent/Resource Reference or Source Identifier or Catalog Number CMV-TNF-Zdk-2xCv This work CMV-TNF-Zdk-2xSca This work Str-KDEL_SBP-2xSca-GPI This work Str-KDEL_SBP-2NGVSVG This work Chemicals, Enzymes and other reagents D-MEM(High Glucose) FUJIFILM Wako Chemicals 045-30285 Penicillin-StreptomycinL-Glutamine Solution (×100) FUJIFILM Wako Chemicals 161-23201 100mmol/L Sodium Pyruvate FUJIFILM Wako Chemicals 190-14881 1 mol/l-HEPES Buffer Nacalai Tesque 17557-94 Fetal Bovine Serum Nichirei 174012 Dynasore Cayman Chemicals 14062 Nocodazole Cayman Chemicals 13857 Cycloheximide Cayman Chemicals 14126 Dynole 34-2 Abcam 120464 Dynole 31-2 Abcam 120474 Dyngo-4a Cayman Chemicals 29479 Biotin FUJIFILM Wako Chemicals 029-08713 Biliverdine TRC B386400 ibidi® μ-Slide 8-well ibidi 80826 JetPrime Polyplus 101000015 JetOptimus Polyplus 101000006 G418 sulfate FUJIFILM Wako Chemicals 078-05961 Puromycin Dihydrochloride FUJIFILM Wako Chemicals 160-23151 2% uranyl acetate Electron Microscopy Sciences 22400-2 8% glutaraldehyde Electron Microscopy Sciences 16000 16% paraformaldehyde Electron Microscopy Sciences 15700 4% osmium tetroxide Electron Microscopy Sciences 19100 EPON-812 Electron Microscopy Sciences 14900 Aclar-film Nisshin-EM 453 Soium cacodylate FUJIFILM Wako Chemicals 194-04852 DAB(3,3’Diaminobenzidine Tetrahydrochloride) FUJIFILM Wako Chemicals 349-00903 Hydrogen Peroxide FUJIFILM Wako Chemicals 081-04215 Software Fiji/ImageJ https://imagej.net/software/ fiji/ Volocity https://www.volocity4d.com Other FV3000 https://www.olympuslifescience.com/ja/laserscanning/fv3000/ SCLIM Kurokawa et al, 2013 10 EMBO reports © The Author(s) D ow nloaded from https://w w w .em bopress.org on D ecem ber 12, 2024 from IP 27.34.65.10. .. Reagent/Resource Reference or Source Identifier or Catalog Number Ultramicrotome EM UC7 Leica SEM Regulus8240 Hitachi TEM JEM1400 JEOL Construction of plasmids for RudLOV and organelle markers The fluorescent tags described herein, Clover, Ruby, NeonGreen, and Scarlet, are tandem repeats of two identical fluorescent proteins, mClover3, mRuby3 (gift from Michael Lin; (Bajar et al, 2016), and mNeonGreen and mScarlet-I (gift from Erik Dent; (Taylor et al, 2020), respectively.
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