Saline:Article Title: In situ cryo-ET of mammalian embryos reveals cytoplasmic lattices contain ubiquitin-charged E2-E3 ligase assemblies
Article Snippet: .. Mouse embryos were fixed in 4% methanol-free formaldehyde (Thermo Scientific; #28906) in phosphate-buffered saline (PBS) for 20 min at room temperature. .. Fixed embryos were permea-bilized in PBS containing 0.2% Triton X-100 for 10 min at room temperature, then blocked in 1% BSA (Fisher BioReagents; BP1605-100) in PBS overnight at 4°C.
Immunofluorescence:
Microscopy:
Sequencing:Article Title: Chromosomal instability promotes cell migration and invasion via EFEMP1 secretion into extracellular vesicles.
Article Snippet: EFEMP1 (Fibulin-3/ EFEMP1) Novus Biologicals Cat# NBP1-77040, polyclonal STAT1 (Stat1) antibody Cell Signaling Technology Cat# 9172 (9172S), polyclonal, RRID:AB_2198300 © The Author(s) The EMBO Journal 9 Reagent/Resource Reference or Source Identifier or Catalog Number CD63 (H5C6) Mouse mAb Novus Biologicals Cat# NBP2-42225, Clone H5C6, RRID:AB_2884028 CD81 (1D6) Mouse mAb Novus Biologicals Cat# NB100-65805 (: NB10065805SS is the same catalog line), Clone 1D6, RRID:AB_962702 Vinculin (hVIN-1) Mouse mAb Sigma-Aldrich Cat# V9131, Clone hVIN-1, RRID:AB_477629 Calnexin antibody Novus Biologicals Cat# NB100-1965 (NB1001965SS is the same catalog line), RRID:AB_10002123. .. Oligonucleotides and other sequence-based reagents qPCR primers This study Table EV2 shRNA primers This study Table EV2 RAB27A siRNA1 Dharmacon D004667-01-0020 (5′- GGACAAAGUCUGCAAGUUA) RAB27A siRNA2 Dharmacon D004667-04-0020 (5′- GCAACAGCCUCAAGAAUUA) siGENOME nontargeting siRNA Control Pools #2 Dharmacon D001210-02-20 Chemicals, Enzymes and other reagents RPMI 1640 Gibco 11554526 DMEM Gibco 31966-021 Fetal bovine serum, FBS Thermo Fisher Scientific 11573397 Penicillin/ Streptomycin Gibco 15140-122 TrypLE Express Gibco 12605-010 PBS Gibco 12559069 Formaldehyde 4% Sigma-Aldrich 252549 Triton X-100 Sigma-Aldrich 9036-19-5 Phalloidin-iFluor 555 Abcam ab176756 DAPI Sigma D9542-1MG Vivaspin 20 centrifugal concentrator, 100 kDa MWCO PES Cytiva 28-9323-63 qEV single-use EV SEC columns Izon Science IC2-35 Vivaspin 2, 10 kDa MWCO Cytiva 28-9322-47 PKH26 Red Fluorescent Cell Linker Kit Sigma MINI26-1KT EdU Lumiprobe 10540 Click chemistry detection reagent Lumiprobe D1330 c0mplete, EDTAfree Roche 11873580001 Pierce BCA Protein Assay Kit Thermo Scientific 23225 Reagent/Resource Reference or Source Identifier or Catalog Number SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific 10095983 Trans-well chambers/Millicell inserts cellQART 9328002 ECM gel/Matrigel Corning 356234 Doxycycline Sigma-Aldrich D9891 Proteinase K Roche Lot 30032017 BbsI NEB R3539S AgeI NEB R3552 EcoRI NEB Cat# R0101 Polybrene Sigma-Aldrich Cat# 107689 0.45 μm filter TPP Y99745 RNeasy Plus kit Qiage 74136 LunaScript RT SuperMix NEB M3010X iTaq Universal SYBR Green Supermix Bio-Rad 1725124 NEBNext Multiplex Oligos for Illumina NEB E6440L Human fibronectin CellSystems 5050 Mouse laminin Thermo Fisher 23017015 Poly-L-lysine, high MW Sigma-Aldrich A3890401 Hyaluronic acid, high MW Calbiochem 23017015 Rat tail collagen coating solution Merck Life Science N.V 122-20 T7 DNA ligase NEB M0318 T4 PNK NEB M0201 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher 13778075 Software ImageJ v1.53 ImageJ/NIH (ImageJ.net) Fiji ImageJ v1.53c Fiji/ImageJ (ImageJ.net) ZetaView software v8.04.02 Particle Metrix ICY version Xpro Institut Pasteur PEAKS Studio Bioinformatics Solutions Inc. version Xpro Morpheus Broad Institute; heatmaps FunRich v3.1.4 FunRich 10 The EMBO Journal © The Author(s) Reagent/Resource Reference or Source Identifier or Catalog Number ShinyGO (v0.80) South Dakota State University (ShinyGO server) — ShinyGO v0.80 site. ..
Real-time Polymerase Chain Reaction:Article Title: Chromosomal instability promotes cell migration and invasion via EFEMP1 secretion into extracellular vesicles.
Article Snippet: EFEMP1 (Fibulin-3/ EFEMP1) Novus Biologicals Cat# NBP1-77040, polyclonal STAT1 (Stat1) antibody Cell Signaling Technology Cat# 9172 (9172S), polyclonal, RRID:AB_2198300 © The Author(s) The EMBO Journal 9 Reagent/Resource Reference or Source Identifier or Catalog Number CD63 (H5C6) Mouse mAb Novus Biologicals Cat# NBP2-42225, Clone H5C6, RRID:AB_2884028 CD81 (1D6) Mouse mAb Novus Biologicals Cat# NB100-65805 (: NB10065805SS is the same catalog line), Clone 1D6, RRID:AB_962702 Vinculin (hVIN-1) Mouse mAb Sigma-Aldrich Cat# V9131, Clone hVIN-1, RRID:AB_477629 Calnexin antibody Novus Biologicals Cat# NB100-1965 (NB1001965SS is the same catalog line), RRID:AB_10002123. .. Oligonucleotides and other sequence-based reagents qPCR primers This study Table EV2 shRNA primers This study Table EV2 RAB27A siRNA1 Dharmacon D004667-01-0020 (5′- GGACAAAGUCUGCAAGUUA) RAB27A siRNA2 Dharmacon D004667-04-0020 (5′- GCAACAGCCUCAAGAAUUA) siGENOME nontargeting siRNA Control Pools #2 Dharmacon D001210-02-20 Chemicals, Enzymes and other reagents RPMI 1640 Gibco 11554526 DMEM Gibco 31966-021 Fetal bovine serum, FBS Thermo Fisher Scientific 11573397 Penicillin/ Streptomycin Gibco 15140-122 TrypLE Express Gibco 12605-010 PBS Gibco 12559069 Formaldehyde 4% Sigma-Aldrich 252549 Triton X-100 Sigma-Aldrich 9036-19-5 Phalloidin-iFluor 555 Abcam ab176756 DAPI Sigma D9542-1MG Vivaspin 20 centrifugal concentrator, 100 kDa MWCO PES Cytiva 28-9323-63 qEV single-use EV SEC columns Izon Science IC2-35 Vivaspin 2, 10 kDa MWCO Cytiva 28-9322-47 PKH26 Red Fluorescent Cell Linker Kit Sigma MINI26-1KT EdU Lumiprobe 10540 Click chemistry detection reagent Lumiprobe D1330 c0mplete, EDTAfree Roche 11873580001 Pierce BCA Protein Assay Kit Thermo Scientific 23225 Reagent/Resource Reference or Source Identifier or Catalog Number SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific 10095983 Trans-well chambers/Millicell inserts cellQART 9328002 ECM gel/Matrigel Corning 356234 Doxycycline Sigma-Aldrich D9891 Proteinase K Roche Lot 30032017 BbsI NEB R3539S AgeI NEB R3552 EcoRI NEB Cat# R0101 Polybrene Sigma-Aldrich Cat# 107689 0.45 μm filter TPP Y99745 RNeasy Plus kit Qiage 74136 LunaScript RT SuperMix NEB M3010X iTaq Universal SYBR Green Supermix Bio-Rad 1725124 NEBNext Multiplex Oligos for Illumina NEB E6440L Human fibronectin CellSystems 5050 Mouse laminin Thermo Fisher 23017015 Poly-L-lysine, high MW Sigma-Aldrich A3890401 Hyaluronic acid, high MW Calbiochem 23017015 Rat tail collagen coating solution Merck Life Science N.V 122-20 T7 DNA ligase NEB M0318 T4 PNK NEB M0201 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher 13778075 Software ImageJ v1.53 ImageJ/NIH (ImageJ.net) Fiji ImageJ v1.53c Fiji/ImageJ (ImageJ.net) ZetaView software v8.04.02 Particle Metrix ICY version Xpro Institut Pasteur PEAKS Studio Bioinformatics Solutions Inc. version Xpro Morpheus Broad Institute; heatmaps FunRich v3.1.4 FunRich 10 The EMBO Journal © The Author(s) Reagent/Resource Reference or Source Identifier or Catalog Number ShinyGO (v0.80) South Dakota State University (ShinyGO server) — ShinyGO v0.80 site. ..
shRNA:Article Title: Chromosomal instability promotes cell migration and invasion via EFEMP1 secretion into extracellular vesicles.
Article Snippet: EFEMP1 (Fibulin-3/ EFEMP1) Novus Biologicals Cat# NBP1-77040, polyclonal STAT1 (Stat1) antibody Cell Signaling Technology Cat# 9172 (9172S), polyclonal, RRID:AB_2198300 © The Author(s) The EMBO Journal 9 Reagent/Resource Reference or Source Identifier or Catalog Number CD63 (H5C6) Mouse mAb Novus Biologicals Cat# NBP2-42225, Clone H5C6, RRID:AB_2884028 CD81 (1D6) Mouse mAb Novus Biologicals Cat# NB100-65805 (: NB10065805SS is the same catalog line), Clone 1D6, RRID:AB_962702 Vinculin (hVIN-1) Mouse mAb Sigma-Aldrich Cat# V9131, Clone hVIN-1, RRID:AB_477629 Calnexin antibody Novus Biologicals Cat# NB100-1965 (NB1001965SS is the same catalog line), RRID:AB_10002123. .. Oligonucleotides and other sequence-based reagents qPCR primers This study Table EV2 shRNA primers This study Table EV2 RAB27A siRNA1 Dharmacon D004667-01-0020 (5′- GGACAAAGUCUGCAAGUUA) RAB27A siRNA2 Dharmacon D004667-04-0020 (5′- GCAACAGCCUCAAGAAUUA) siGENOME nontargeting siRNA Control Pools #2 Dharmacon D001210-02-20 Chemicals, Enzymes and other reagents RPMI 1640 Gibco 11554526 DMEM Gibco 31966-021 Fetal bovine serum, FBS Thermo Fisher Scientific 11573397 Penicillin/ Streptomycin Gibco 15140-122 TrypLE Express Gibco 12605-010 PBS Gibco 12559069 Formaldehyde 4% Sigma-Aldrich 252549 Triton X-100 Sigma-Aldrich 9036-19-5 Phalloidin-iFluor 555 Abcam ab176756 DAPI Sigma D9542-1MG Vivaspin 20 centrifugal concentrator, 100 kDa MWCO PES Cytiva 28-9323-63 qEV single-use EV SEC columns Izon Science IC2-35 Vivaspin 2, 10 kDa MWCO Cytiva 28-9322-47 PKH26 Red Fluorescent Cell Linker Kit Sigma MINI26-1KT EdU Lumiprobe 10540 Click chemistry detection reagent Lumiprobe D1330 c0mplete, EDTAfree Roche 11873580001 Pierce BCA Protein Assay Kit Thermo Scientific 23225 Reagent/Resource Reference or Source Identifier or Catalog Number SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific 10095983 Trans-well chambers/Millicell inserts cellQART 9328002 ECM gel/Matrigel Corning 356234 Doxycycline Sigma-Aldrich D9891 Proteinase K Roche Lot 30032017 BbsI NEB R3539S AgeI NEB R3552 EcoRI NEB Cat# R0101 Polybrene Sigma-Aldrich Cat# 107689 0.45 μm filter TPP Y99745 RNeasy Plus kit Qiage 74136 LunaScript RT SuperMix NEB M3010X iTaq Universal SYBR Green Supermix Bio-Rad 1725124 NEBNext Multiplex Oligos for Illumina NEB E6440L Human fibronectin CellSystems 5050 Mouse laminin Thermo Fisher 23017015 Poly-L-lysine, high MW Sigma-Aldrich A3890401 Hyaluronic acid, high MW Calbiochem 23017015 Rat tail collagen coating solution Merck Life Science N.V 122-20 T7 DNA ligase NEB M0318 T4 PNK NEB M0201 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher 13778075 Software ImageJ v1.53 ImageJ/NIH (ImageJ.net) Fiji ImageJ v1.53c Fiji/ImageJ (ImageJ.net) ZetaView software v8.04.02 Particle Metrix ICY version Xpro Institut Pasteur PEAKS Studio Bioinformatics Solutions Inc. version Xpro Morpheus Broad Institute; heatmaps FunRich v3.1.4 FunRich 10 The EMBO Journal © The Author(s) Reagent/Resource Reference or Source Identifier or Catalog Number ShinyGO (v0.80) South Dakota State University (ShinyGO server) — ShinyGO v0.80 site. ..
Control:Article Title: Chromosomal instability promotes cell migration and invasion via EFEMP1 secretion into extracellular vesicles.
Article Snippet: EFEMP1 (Fibulin-3/ EFEMP1) Novus Biologicals Cat# NBP1-77040, polyclonal STAT1 (Stat1) antibody Cell Signaling Technology Cat# 9172 (9172S), polyclonal, RRID:AB_2198300 © The Author(s) The EMBO Journal 9 Reagent/Resource Reference or Source Identifier or Catalog Number CD63 (H5C6) Mouse mAb Novus Biologicals Cat# NBP2-42225, Clone H5C6, RRID:AB_2884028 CD81 (1D6) Mouse mAb Novus Biologicals Cat# NB100-65805 (: NB10065805SS is the same catalog line), Clone 1D6, RRID:AB_962702 Vinculin (hVIN-1) Mouse mAb Sigma-Aldrich Cat# V9131, Clone hVIN-1, RRID:AB_477629 Calnexin antibody Novus Biologicals Cat# NB100-1965 (NB1001965SS is the same catalog line), RRID:AB_10002123. .. Oligonucleotides and other sequence-based reagents qPCR primers This study Table EV2 shRNA primers This study Table EV2 RAB27A siRNA1 Dharmacon D004667-01-0020 (5′- GGACAAAGUCUGCAAGUUA) RAB27A siRNA2 Dharmacon D004667-04-0020 (5′- GCAACAGCCUCAAGAAUUA) siGENOME nontargeting siRNA Control Pools #2 Dharmacon D001210-02-20 Chemicals, Enzymes and other reagents RPMI 1640 Gibco 11554526 DMEM Gibco 31966-021 Fetal bovine serum, FBS Thermo Fisher Scientific 11573397 Penicillin/ Streptomycin Gibco 15140-122 TrypLE Express Gibco 12605-010 PBS Gibco 12559069 Formaldehyde 4% Sigma-Aldrich 252549 Triton X-100 Sigma-Aldrich 9036-19-5 Phalloidin-iFluor 555 Abcam ab176756 DAPI Sigma D9542-1MG Vivaspin 20 centrifugal concentrator, 100 kDa MWCO PES Cytiva 28-9323-63 qEV single-use EV SEC columns Izon Science IC2-35 Vivaspin 2, 10 kDa MWCO Cytiva 28-9322-47 PKH26 Red Fluorescent Cell Linker Kit Sigma MINI26-1KT EdU Lumiprobe 10540 Click chemistry detection reagent Lumiprobe D1330 c0mplete, EDTAfree Roche 11873580001 Pierce BCA Protein Assay Kit Thermo Scientific 23225 Reagent/Resource Reference or Source Identifier or Catalog Number SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific 10095983 Trans-well chambers/Millicell inserts cellQART 9328002 ECM gel/Matrigel Corning 356234 Doxycycline Sigma-Aldrich D9891 Proteinase K Roche Lot 30032017 BbsI NEB R3539S AgeI NEB R3552 EcoRI NEB Cat# R0101 Polybrene Sigma-Aldrich Cat# 107689 0.45 μm filter TPP Y99745 RNeasy Plus kit Qiage 74136 LunaScript RT SuperMix NEB M3010X iTaq Universal SYBR Green Supermix Bio-Rad 1725124 NEBNext Multiplex Oligos for Illumina NEB E6440L Human fibronectin CellSystems 5050 Mouse laminin Thermo Fisher 23017015 Poly-L-lysine, high MW Sigma-Aldrich A3890401 Hyaluronic acid, high MW Calbiochem 23017015 Rat tail collagen coating solution Merck Life Science N.V 122-20 T7 DNA ligase NEB M0318 T4 PNK NEB M0201 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher 13778075 Software ImageJ v1.53 ImageJ/NIH (ImageJ.net) Fiji ImageJ v1.53c Fiji/ImageJ (ImageJ.net) ZetaView software v8.04.02 Particle Metrix ICY version Xpro Institut Pasteur PEAKS Studio Bioinformatics Solutions Inc. version Xpro Morpheus Broad Institute; heatmaps FunRich v3.1.4 FunRich 10 The EMBO Journal © The Author(s) Reagent/Resource Reference or Source Identifier or Catalog Number ShinyGO (v0.80) South Dakota State University (ShinyGO server) — ShinyGO v0.80 site. ..
Size-exclusion Chromatography:Article Title: Chromosomal instability promotes cell migration and invasion via EFEMP1 secretion into extracellular vesicles.
Article Snippet: EFEMP1 (Fibulin-3/ EFEMP1) Novus Biologicals Cat# NBP1-77040, polyclonal STAT1 (Stat1) antibody Cell Signaling Technology Cat# 9172 (9172S), polyclonal, RRID:AB_2198300 © The Author(s) The EMBO Journal 9 Reagent/Resource Reference or Source Identifier or Catalog Number CD63 (H5C6) Mouse mAb Novus Biologicals Cat# NBP2-42225, Clone H5C6, RRID:AB_2884028 CD81 (1D6) Mouse mAb Novus Biologicals Cat# NB100-65805 (: NB10065805SS is the same catalog line), Clone 1D6, RRID:AB_962702 Vinculin (hVIN-1) Mouse mAb Sigma-Aldrich Cat# V9131, Clone hVIN-1, RRID:AB_477629 Calnexin antibody Novus Biologicals Cat# NB100-1965 (NB1001965SS is the same catalog line), RRID:AB_10002123. .. Oligonucleotides and other sequence-based reagents qPCR primers This study Table EV2 shRNA primers This study Table EV2 RAB27A siRNA1 Dharmacon D004667-01-0020 (5′- GGACAAAGUCUGCAAGUUA) RAB27A siRNA2 Dharmacon D004667-04-0020 (5′- GCAACAGCCUCAAGAAUUA) siGENOME nontargeting siRNA Control Pools #2 Dharmacon D001210-02-20 Chemicals, Enzymes and other reagents RPMI 1640 Gibco 11554526 DMEM Gibco 31966-021 Fetal bovine serum, FBS Thermo Fisher Scientific 11573397 Penicillin/ Streptomycin Gibco 15140-122 TrypLE Express Gibco 12605-010 PBS Gibco 12559069 Formaldehyde 4% Sigma-Aldrich 252549 Triton X-100 Sigma-Aldrich 9036-19-5 Phalloidin-iFluor 555 Abcam ab176756 DAPI Sigma D9542-1MG Vivaspin 20 centrifugal concentrator, 100 kDa MWCO PES Cytiva 28-9323-63 qEV single-use EV SEC columns Izon Science IC2-35 Vivaspin 2, 10 kDa MWCO Cytiva 28-9322-47 PKH26 Red Fluorescent Cell Linker Kit Sigma MINI26-1KT EdU Lumiprobe 10540 Click chemistry detection reagent Lumiprobe D1330 c0mplete, EDTAfree Roche 11873580001 Pierce BCA Protein Assay Kit Thermo Scientific 23225 Reagent/Resource Reference or Source Identifier or Catalog Number SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific 10095983 Trans-well chambers/Millicell inserts cellQART 9328002 ECM gel/Matrigel Corning 356234 Doxycycline Sigma-Aldrich D9891 Proteinase K Roche Lot 30032017 BbsI NEB R3539S AgeI NEB R3552 EcoRI NEB Cat# R0101 Polybrene Sigma-Aldrich Cat# 107689 0.45 μm filter TPP Y99745 RNeasy Plus kit Qiage 74136 LunaScript RT SuperMix NEB M3010X iTaq Universal SYBR Green Supermix Bio-Rad 1725124 NEBNext Multiplex Oligos for Illumina NEB E6440L Human fibronectin CellSystems 5050 Mouse laminin Thermo Fisher 23017015 Poly-L-lysine, high MW Sigma-Aldrich A3890401 Hyaluronic acid, high MW Calbiochem 23017015 Rat tail collagen coating solution Merck Life Science N.V 122-20 T7 DNA ligase NEB M0318 T4 PNK NEB M0201 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher 13778075 Software ImageJ v1.53 ImageJ/NIH (ImageJ.net) Fiji ImageJ v1.53c Fiji/ImageJ (ImageJ.net) ZetaView software v8.04.02 Particle Metrix ICY version Xpro Institut Pasteur PEAKS Studio Bioinformatics Solutions Inc. version Xpro Morpheus Broad Institute; heatmaps FunRich v3.1.4 FunRich 10 The EMBO Journal © The Author(s) Reagent/Resource Reference or Source Identifier or Catalog Number ShinyGO (v0.80) South Dakota State University (ShinyGO server) — ShinyGO v0.80 site. ..
Bicinchoninic Acid Protein Assay:Article Title: Chromosomal instability promotes cell migration and invasion via EFEMP1 secretion into extracellular vesicles.
Article Snippet: EFEMP1 (Fibulin-3/ EFEMP1) Novus Biologicals Cat# NBP1-77040, polyclonal STAT1 (Stat1) antibody Cell Signaling Technology Cat# 9172 (9172S), polyclonal, RRID:AB_2198300 © The Author(s) The EMBO Journal 9 Reagent/Resource Reference or Source Identifier or Catalog Number CD63 (H5C6) Mouse mAb Novus Biologicals Cat# NBP2-42225, Clone H5C6, RRID:AB_2884028 CD81 (1D6) Mouse mAb Novus Biologicals Cat# NB100-65805 (: NB10065805SS is the same catalog line), Clone 1D6, RRID:AB_962702 Vinculin (hVIN-1) Mouse mAb Sigma-Aldrich Cat# V9131, Clone hVIN-1, RRID:AB_477629 Calnexin antibody Novus Biologicals Cat# NB100-1965 (NB1001965SS is the same catalog line), RRID:AB_10002123. .. Oligonucleotides and other sequence-based reagents qPCR primers This study Table EV2 shRNA primers This study Table EV2 RAB27A siRNA1 Dharmacon D004667-01-0020 (5′- GGACAAAGUCUGCAAGUUA) RAB27A siRNA2 Dharmacon D004667-04-0020 (5′- GCAACAGCCUCAAGAAUUA) siGENOME nontargeting siRNA Control Pools #2 Dharmacon D001210-02-20 Chemicals, Enzymes and other reagents RPMI 1640 Gibco 11554526 DMEM Gibco 31966-021 Fetal bovine serum, FBS Thermo Fisher Scientific 11573397 Penicillin/ Streptomycin Gibco 15140-122 TrypLE Express Gibco 12605-010 PBS Gibco 12559069 Formaldehyde 4% Sigma-Aldrich 252549 Triton X-100 Sigma-Aldrich 9036-19-5 Phalloidin-iFluor 555 Abcam ab176756 DAPI Sigma D9542-1MG Vivaspin 20 centrifugal concentrator, 100 kDa MWCO PES Cytiva 28-9323-63 qEV single-use EV SEC columns Izon Science IC2-35 Vivaspin 2, 10 kDa MWCO Cytiva 28-9322-47 PKH26 Red Fluorescent Cell Linker Kit Sigma MINI26-1KT EdU Lumiprobe 10540 Click chemistry detection reagent Lumiprobe D1330 c0mplete, EDTAfree Roche 11873580001 Pierce BCA Protein Assay Kit Thermo Scientific 23225 Reagent/Resource Reference or Source Identifier or Catalog Number SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific 10095983 Trans-well chambers/Millicell inserts cellQART 9328002 ECM gel/Matrigel Corning 356234 Doxycycline Sigma-Aldrich D9891 Proteinase K Roche Lot 30032017 BbsI NEB R3539S AgeI NEB R3552 EcoRI NEB Cat# R0101 Polybrene Sigma-Aldrich Cat# 107689 0.45 μm filter TPP Y99745 RNeasy Plus kit Qiage 74136 LunaScript RT SuperMix NEB M3010X iTaq Universal SYBR Green Supermix Bio-Rad 1725124 NEBNext Multiplex Oligos for Illumina NEB E6440L Human fibronectin CellSystems 5050 Mouse laminin Thermo Fisher 23017015 Poly-L-lysine, high MW Sigma-Aldrich A3890401 Hyaluronic acid, high MW Calbiochem 23017015 Rat tail collagen coating solution Merck Life Science N.V 122-20 T7 DNA ligase NEB M0318 T4 PNK NEB M0201 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher 13778075 Software ImageJ v1.53 ImageJ/NIH (ImageJ.net) Fiji ImageJ v1.53c Fiji/ImageJ (ImageJ.net) ZetaView software v8.04.02 Particle Metrix ICY version Xpro Institut Pasteur PEAKS Studio Bioinformatics Solutions Inc. version Xpro Morpheus Broad Institute; heatmaps FunRich v3.1.4 FunRich 10 The EMBO Journal © The Author(s) Reagent/Resource Reference or Source Identifier or Catalog Number ShinyGO (v0.80) South Dakota State University (ShinyGO server) — ShinyGO v0.80 site. ..
SYBR Green Assay:Article Title: Chromosomal instability promotes cell migration and invasion via EFEMP1 secretion into extracellular vesicles.
Article Snippet: EFEMP1 (Fibulin-3/ EFEMP1) Novus Biologicals Cat# NBP1-77040, polyclonal STAT1 (Stat1) antibody Cell Signaling Technology Cat# 9172 (9172S), polyclonal, RRID:AB_2198300 © The Author(s) The EMBO Journal 9 Reagent/Resource Reference or Source Identifier or Catalog Number CD63 (H5C6) Mouse mAb Novus Biologicals Cat# NBP2-42225, Clone H5C6, RRID:AB_2884028 CD81 (1D6) Mouse mAb Novus Biologicals Cat# NB100-65805 (: NB10065805SS is the same catalog line), Clone 1D6, RRID:AB_962702 Vinculin (hVIN-1) Mouse mAb Sigma-Aldrich Cat# V9131, Clone hVIN-1, RRID:AB_477629 Calnexin antibody Novus Biologicals Cat# NB100-1965 (NB1001965SS is the same catalog line), RRID:AB_10002123. .. Oligonucleotides and other sequence-based reagents qPCR primers This study Table EV2 shRNA primers This study Table EV2 RAB27A siRNA1 Dharmacon D004667-01-0020 (5′- GGACAAAGUCUGCAAGUUA) RAB27A siRNA2 Dharmacon D004667-04-0020 (5′- GCAACAGCCUCAAGAAUUA) siGENOME nontargeting siRNA Control Pools #2 Dharmacon D001210-02-20 Chemicals, Enzymes and other reagents RPMI 1640 Gibco 11554526 DMEM Gibco 31966-021 Fetal bovine serum, FBS Thermo Fisher Scientific 11573397 Penicillin/ Streptomycin Gibco 15140-122 TrypLE Express Gibco 12605-010 PBS Gibco 12559069 Formaldehyde 4% Sigma-Aldrich 252549 Triton X-100 Sigma-Aldrich 9036-19-5 Phalloidin-iFluor 555 Abcam ab176756 DAPI Sigma D9542-1MG Vivaspin 20 centrifugal concentrator, 100 kDa MWCO PES Cytiva 28-9323-63 qEV single-use EV SEC columns Izon Science IC2-35 Vivaspin 2, 10 kDa MWCO Cytiva 28-9322-47 PKH26 Red Fluorescent Cell Linker Kit Sigma MINI26-1KT EdU Lumiprobe 10540 Click chemistry detection reagent Lumiprobe D1330 c0mplete, EDTAfree Roche 11873580001 Pierce BCA Protein Assay Kit Thermo Scientific 23225 Reagent/Resource Reference or Source Identifier or Catalog Number SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific 10095983 Trans-well chambers/Millicell inserts cellQART 9328002 ECM gel/Matrigel Corning 356234 Doxycycline Sigma-Aldrich D9891 Proteinase K Roche Lot 30032017 BbsI NEB R3539S AgeI NEB R3552 EcoRI NEB Cat# R0101 Polybrene Sigma-Aldrich Cat# 107689 0.45 μm filter TPP Y99745 RNeasy Plus kit Qiage 74136 LunaScript RT SuperMix NEB M3010X iTaq Universal SYBR Green Supermix Bio-Rad 1725124 NEBNext Multiplex Oligos for Illumina NEB E6440L Human fibronectin CellSystems 5050 Mouse laminin Thermo Fisher 23017015 Poly-L-lysine, high MW Sigma-Aldrich A3890401 Hyaluronic acid, high MW Calbiochem 23017015 Rat tail collagen coating solution Merck Life Science N.V 122-20 T7 DNA ligase NEB M0318 T4 PNK NEB M0201 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher 13778075 Software ImageJ v1.53 ImageJ/NIH (ImageJ.net) Fiji ImageJ v1.53c Fiji/ImageJ (ImageJ.net) ZetaView software v8.04.02 Particle Metrix ICY version Xpro Institut Pasteur PEAKS Studio Bioinformatics Solutions Inc. version Xpro Morpheus Broad Institute; heatmaps FunRich v3.1.4 FunRich 10 The EMBO Journal © The Author(s) Reagent/Resource Reference or Source Identifier or Catalog Number ShinyGO (v0.80) South Dakota State University (ShinyGO server) — ShinyGO v0.80 site. ..
Multiplex Assay:Article Title: Chromosomal instability promotes cell migration and invasion via EFEMP1 secretion into extracellular vesicles.
Article Snippet: EFEMP1 (Fibulin-3/ EFEMP1) Novus Biologicals Cat# NBP1-77040, polyclonal STAT1 (Stat1) antibody Cell Signaling Technology Cat# 9172 (9172S), polyclonal, RRID:AB_2198300 © The Author(s) The EMBO Journal 9 Reagent/Resource Reference or Source Identifier or Catalog Number CD63 (H5C6) Mouse mAb Novus Biologicals Cat# NBP2-42225, Clone H5C6, RRID:AB_2884028 CD81 (1D6) Mouse mAb Novus Biologicals Cat# NB100-65805 (: NB10065805SS is the same catalog line), Clone 1D6, RRID:AB_962702 Vinculin (hVIN-1) Mouse mAb Sigma-Aldrich Cat# V9131, Clone hVIN-1, RRID:AB_477629 Calnexin antibody Novus Biologicals Cat# NB100-1965 (NB1001965SS is the same catalog line), RRID:AB_10002123. .. Oligonucleotides and other sequence-based reagents qPCR primers This study Table EV2 shRNA primers This study Table EV2 RAB27A siRNA1 Dharmacon D004667-01-0020 (5′- GGACAAAGUCUGCAAGUUA) RAB27A siRNA2 Dharmacon D004667-04-0020 (5′- GCAACAGCCUCAAGAAUUA) siGENOME nontargeting siRNA Control Pools #2 Dharmacon D001210-02-20 Chemicals, Enzymes and other reagents RPMI 1640 Gibco 11554526 DMEM Gibco 31966-021 Fetal bovine serum, FBS Thermo Fisher Scientific 11573397 Penicillin/ Streptomycin Gibco 15140-122 TrypLE Express Gibco 12605-010 PBS Gibco 12559069 Formaldehyde 4% Sigma-Aldrich 252549 Triton X-100 Sigma-Aldrich 9036-19-5 Phalloidin-iFluor 555 Abcam ab176756 DAPI Sigma D9542-1MG Vivaspin 20 centrifugal concentrator, 100 kDa MWCO PES Cytiva 28-9323-63 qEV single-use EV SEC columns Izon Science IC2-35 Vivaspin 2, 10 kDa MWCO Cytiva 28-9322-47 PKH26 Red Fluorescent Cell Linker Kit Sigma MINI26-1KT EdU Lumiprobe 10540 Click chemistry detection reagent Lumiprobe D1330 c0mplete, EDTAfree Roche 11873580001 Pierce BCA Protein Assay Kit Thermo Scientific 23225 Reagent/Resource Reference or Source Identifier or Catalog Number SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific 10095983 Trans-well chambers/Millicell inserts cellQART 9328002 ECM gel/Matrigel Corning 356234 Doxycycline Sigma-Aldrich D9891 Proteinase K Roche Lot 30032017 BbsI NEB R3539S AgeI NEB R3552 EcoRI NEB Cat# R0101 Polybrene Sigma-Aldrich Cat# 107689 0.45 μm filter TPP Y99745 RNeasy Plus kit Qiage 74136 LunaScript RT SuperMix NEB M3010X iTaq Universal SYBR Green Supermix Bio-Rad 1725124 NEBNext Multiplex Oligos for Illumina NEB E6440L Human fibronectin CellSystems 5050 Mouse laminin Thermo Fisher 23017015 Poly-L-lysine, high MW Sigma-Aldrich A3890401 Hyaluronic acid, high MW Calbiochem 23017015 Rat tail collagen coating solution Merck Life Science N.V 122-20 T7 DNA ligase NEB M0318 T4 PNK NEB M0201 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher 13778075 Software ImageJ v1.53 ImageJ/NIH (ImageJ.net) Fiji ImageJ v1.53c Fiji/ImageJ (ImageJ.net) ZetaView software v8.04.02 Particle Metrix ICY version Xpro Institut Pasteur PEAKS Studio Bioinformatics Solutions Inc. version Xpro Morpheus Broad Institute; heatmaps FunRich v3.1.4 FunRich 10 The EMBO Journal © The Author(s) Reagent/Resource Reference or Source Identifier or Catalog Number ShinyGO (v0.80) South Dakota State University (ShinyGO server) — ShinyGO v0.80 site. ..
Transfection:Article Title: Chromosomal instability promotes cell migration and invasion via EFEMP1 secretion into extracellular vesicles.
Article Snippet: EFEMP1 (Fibulin-3/ EFEMP1) Novus Biologicals Cat# NBP1-77040, polyclonal STAT1 (Stat1) antibody Cell Signaling Technology Cat# 9172 (9172S), polyclonal, RRID:AB_2198300 © The Author(s) The EMBO Journal 9 Reagent/Resource Reference or Source Identifier or Catalog Number CD63 (H5C6) Mouse mAb Novus Biologicals Cat# NBP2-42225, Clone H5C6, RRID:AB_2884028 CD81 (1D6) Mouse mAb Novus Biologicals Cat# NB100-65805 (: NB10065805SS is the same catalog line), Clone 1D6, RRID:AB_962702 Vinculin (hVIN-1) Mouse mAb Sigma-Aldrich Cat# V9131, Clone hVIN-1, RRID:AB_477629 Calnexin antibody Novus Biologicals Cat# NB100-1965 (NB1001965SS is the same catalog line), RRID:AB_10002123. .. Oligonucleotides and other sequence-based reagents qPCR primers This study Table EV2 shRNA primers This study Table EV2 RAB27A siRNA1 Dharmacon D004667-01-0020 (5′- GGACAAAGUCUGCAAGUUA) RAB27A siRNA2 Dharmacon D004667-04-0020 (5′- GCAACAGCCUCAAGAAUUA) siGENOME nontargeting siRNA Control Pools #2 Dharmacon D001210-02-20 Chemicals, Enzymes and other reagents RPMI 1640 Gibco 11554526 DMEM Gibco 31966-021 Fetal bovine serum, FBS Thermo Fisher Scientific 11573397 Penicillin/ Streptomycin Gibco 15140-122 TrypLE Express Gibco 12605-010 PBS Gibco 12559069 Formaldehyde 4% Sigma-Aldrich 252549 Triton X-100 Sigma-Aldrich 9036-19-5 Phalloidin-iFluor 555 Abcam ab176756 DAPI Sigma D9542-1MG Vivaspin 20 centrifugal concentrator, 100 kDa MWCO PES Cytiva 28-9323-63 qEV single-use EV SEC columns Izon Science IC2-35 Vivaspin 2, 10 kDa MWCO Cytiva 28-9322-47 PKH26 Red Fluorescent Cell Linker Kit Sigma MINI26-1KT EdU Lumiprobe 10540 Click chemistry detection reagent Lumiprobe D1330 c0mplete, EDTAfree Roche 11873580001 Pierce BCA Protein Assay Kit Thermo Scientific 23225 Reagent/Resource Reference or Source Identifier or Catalog Number SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific 10095983 Trans-well chambers/Millicell inserts cellQART 9328002 ECM gel/Matrigel Corning 356234 Doxycycline Sigma-Aldrich D9891 Proteinase K Roche Lot 30032017 BbsI NEB R3539S AgeI NEB R3552 EcoRI NEB Cat# R0101 Polybrene Sigma-Aldrich Cat# 107689 0.45 μm filter TPP Y99745 RNeasy Plus kit Qiage 74136 LunaScript RT SuperMix NEB M3010X iTaq Universal SYBR Green Supermix Bio-Rad 1725124 NEBNext Multiplex Oligos for Illumina NEB E6440L Human fibronectin CellSystems 5050 Mouse laminin Thermo Fisher 23017015 Poly-L-lysine, high MW Sigma-Aldrich A3890401 Hyaluronic acid, high MW Calbiochem 23017015 Rat tail collagen coating solution Merck Life Science N.V 122-20 T7 DNA ligase NEB M0318 T4 PNK NEB M0201 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher 13778075 Software ImageJ v1.53 ImageJ/NIH (ImageJ.net) Fiji ImageJ v1.53c Fiji/ImageJ (ImageJ.net) ZetaView software v8.04.02 Particle Metrix ICY version Xpro Institut Pasteur PEAKS Studio Bioinformatics Solutions Inc. version Xpro Morpheus Broad Institute; heatmaps FunRich v3.1.4 FunRich 10 The EMBO Journal © The Author(s) Reagent/Resource Reference or Source Identifier or Catalog Number ShinyGO (v0.80) South Dakota State University (ShinyGO server) — ShinyGO v0.80 site. ..
Software:Article Title: Chromosomal instability promotes cell migration and invasion via EFEMP1 secretion into extracellular vesicles.
Article Snippet: EFEMP1 (Fibulin-3/ EFEMP1) Novus Biologicals Cat# NBP1-77040, polyclonal STAT1 (Stat1) antibody Cell Signaling Technology Cat# 9172 (9172S), polyclonal, RRID:AB_2198300 © The Author(s) The EMBO Journal 9 Reagent/Resource Reference or Source Identifier or Catalog Number CD63 (H5C6) Mouse mAb Novus Biologicals Cat# NBP2-42225, Clone H5C6, RRID:AB_2884028 CD81 (1D6) Mouse mAb Novus Biologicals Cat# NB100-65805 (: NB10065805SS is the same catalog line), Clone 1D6, RRID:AB_962702 Vinculin (hVIN-1) Mouse mAb Sigma-Aldrich Cat# V9131, Clone hVIN-1, RRID:AB_477629 Calnexin antibody Novus Biologicals Cat# NB100-1965 (NB1001965SS is the same catalog line), RRID:AB_10002123. .. Oligonucleotides and other sequence-based reagents qPCR primers This study Table EV2 shRNA primers This study Table EV2 RAB27A siRNA1 Dharmacon D004667-01-0020 (5′- GGACAAAGUCUGCAAGUUA) RAB27A siRNA2 Dharmacon D004667-04-0020 (5′- GCAACAGCCUCAAGAAUUA) siGENOME nontargeting siRNA Control Pools #2 Dharmacon D001210-02-20 Chemicals, Enzymes and other reagents RPMI 1640 Gibco 11554526 DMEM Gibco 31966-021 Fetal bovine serum, FBS Thermo Fisher Scientific 11573397 Penicillin/ Streptomycin Gibco 15140-122 TrypLE Express Gibco 12605-010 PBS Gibco 12559069 Formaldehyde 4% Sigma-Aldrich 252549 Triton X-100 Sigma-Aldrich 9036-19-5 Phalloidin-iFluor 555 Abcam ab176756 DAPI Sigma D9542-1MG Vivaspin 20 centrifugal concentrator, 100 kDa MWCO PES Cytiva 28-9323-63 qEV single-use EV SEC columns Izon Science IC2-35 Vivaspin 2, 10 kDa MWCO Cytiva 28-9322-47 PKH26 Red Fluorescent Cell Linker Kit Sigma MINI26-1KT EdU Lumiprobe 10540 Click chemistry detection reagent Lumiprobe D1330 c0mplete, EDTAfree Roche 11873580001 Pierce BCA Protein Assay Kit Thermo Scientific 23225 Reagent/Resource Reference or Source Identifier or Catalog Number SuperSignal West Femto Maximum Sensitivity Substrate Thermo Fisher Scientific 10095983 Trans-well chambers/Millicell inserts cellQART 9328002 ECM gel/Matrigel Corning 356234 Doxycycline Sigma-Aldrich D9891 Proteinase K Roche Lot 30032017 BbsI NEB R3539S AgeI NEB R3552 EcoRI NEB Cat# R0101 Polybrene Sigma-Aldrich Cat# 107689 0.45 μm filter TPP Y99745 RNeasy Plus kit Qiage 74136 LunaScript RT SuperMix NEB M3010X iTaq Universal SYBR Green Supermix Bio-Rad 1725124 NEBNext Multiplex Oligos for Illumina NEB E6440L Human fibronectin CellSystems 5050 Mouse laminin Thermo Fisher 23017015 Poly-L-lysine, high MW Sigma-Aldrich A3890401 Hyaluronic acid, high MW Calbiochem 23017015 Rat tail collagen coating solution Merck Life Science N.V 122-20 T7 DNA ligase NEB M0318 T4 PNK NEB M0201 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher 13778075 Software ImageJ v1.53 ImageJ/NIH (ImageJ.net) Fiji ImageJ v1.53c Fiji/ImageJ (ImageJ.net) ZetaView software v8.04.02 Particle Metrix ICY version Xpro Institut Pasteur PEAKS Studio Bioinformatics Solutions Inc. version Xpro Morpheus Broad Institute; heatmaps FunRich v3.1.4 FunRich 10 The EMBO Journal © The Author(s) Reagent/Resource Reference or Source Identifier or Catalog Number ShinyGO (v0.80) South Dakota State University (ShinyGO server) — ShinyGO v0.80 site. ..
Incubation:Article Title: Cytoplasmic localization of pseudouridine synthase 7 facilitates a pseudouridine-dependent enhancement of cellular stress tolerance.
Article Snippet: After approximately 4 days, the cultures reached ~70% confluency, and cells were sub-cultured into 6-well plates coated with Type 1 collagen (Advanced AR TI CL E IN P RE SS BioMatrix, Cat#5005) and allowed to attach to the growth surface for 24 hours before exposure to particulate matter. .. Following exposure, cells were washed with pre-warmed PBS for 5 min, then fixed by incubation for 15 min at 37°C in a freshly prepared, methanol-free 4% formaldehyde solution (Thermo Scientific, 28906) in PBS. .. The PUS7 insert sequence was reverse transcribed from total RNA and inserted into the AAV-CMV-eGFP plasmid (Addgene, Plasmid #193022).
Gentle:Article Title: Engineering autologous ossicles for the personalized modeling of acute myeloid leukemia
Article Snippet: .. Tissues were fixed in 4% formaldehyde (Thermo Scientific) at 4°C, for 12 h, washed three times in PBS 1X, and decalcified with 10% EDTA solution (Sigma-Aldrich), pH 8 up to 2 weeks with gentle rocking, at 4°C. ..
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