SYBR Green Assay:Article Title: Analyzing embryo dormancy at single-cell resolution reveals dynamic transcriptional responses and activation of integrin-Yap/Taz prosurvival signaling.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Non-essential amino acids Sigma-Aldrich Cat# M7145 Penicillin-streptomycin Sigma-Aldrich Cat# P4333 N2 Thermo Fisher Scientific Cat# 17502048 B27 without vitamin A Thermo Fisher Scientific Cat# 12587001 Trypsin-EDTA (0.25%) Sigma-Aldrich Cat# 25200056 2-mercaptoethanol Sigma-Aldrich Cat# M7522 Formaldehyde (w/v), methanol-free 16% Thermo Fisher Cat# 28908 Triton X-100 Sigma-Aldrich Cat# T9284 PBS without Ca/Mg Sigma-Aldrich Cat# D8537 iTag SYBR green supermix Bio-Rad Cat# 1725120 GoTaq green master mix Promega Cat# M7123 Precision Plus Protein Kaleidoscope protein standard Bio-Rad Cat# 161-0375 PD0325901 Cayman Chemical Cat# 13034 CHIR99021 Tocris Cat# 4423 human Lif homemade A kind gift from Prof. Hans R. Schöler, Max Planck Institute for Molecular Biomedicine, M€unster, Germany Lipophectamine 2000 Thermo Fisher Scientific Cat# 11668027 Doxycyclin Sigma-Aldrich Cat# D9891 4-hydroxytamoxifen (4-OHT) Sigma-Aldrich Cat# H7904 Neomycin Sigma-Aldrich Cat# G8168 Gelatin solution Sigma-Aldrich Cat# 1393 ECL Western Blotting Detection Reagent GE Healthcare Cat# RPN2109 ECL Prime Western Blotting Detection Reagent GE Healthcare Cat# RPN2232 PVDF membrane Millipore Cat# IPVH00010 Mineral oil, embryo-tested Sigma-Aldrich Cat# M5310 PMSF Sigma-Aldrich Cat# P7626 Donkey serum VMR Cat# S2170 PMSG Ceva N/A HCG Ceva N/A Depo Clinovir Pfizer N/A b-estradiol Sigma-Aldrich E8875 M2 medium Sigma-Aldrich Cat# M7167 KSOM Millipore Cat# MR-020P-5F Tamoxifen Sigma-Aldrich Cat# T5648 DMSO Carl Roth Cat# A994.1 Tween 20 Sigma-Aldrich Cat# P7949 Corn oil Sigma-Aldrich Cat# C8267 Tyrode’s solution, Acidic Sigma-Aldrich Cat# T1788 TrypLE Express Enzyme Thermo Fisher Scientific Cat# 12604013 Methanol anhydrous 99.8% Sigma-Aldrich Cat# 322415-100ML Benzyl Alcohol Sigma-Aldrich Cat# 24122-2.5L-M Benzyl Benzoate 99+% Thermo Fisher Scientific Cat# 105860010 Heparin sodium salt Sigma-Aldrich Cat# 3149 Glycine Sigma-Aldrich Cat# G7126 Sodium deoxycholate Sigma-Aldrich Cat# 30970 Critical commercial assays In-Fusion HD cloning kit Clontech Cat# 638909 m-Slide 8 Well Ibidi Cat# 80826 (Continued on next page) e2 Cell Stem Cell 31, 1–18.e1–e8, September 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides see Table S4 N/A Recombinant DNA PyCAG-PBase Wang et al.53 N/A pPB-CAG-rtTAM2-IN Adachi et al.54 N/A pPB-CAG-CreERT2-IRES-Neo Adachi et al.54 N/A pPB-hCMV1-Bik-IRES-Venus This paper N/A pPB-hCMV1-mutBik-IRES-Venus This paper N/A pPB-hCMV1-Bcl2-IRES-Venus This paper N/A pPB-CAG-HA-IRES-Venus This paper N/A pPB-CAG-mYap mut aa112 S to A-IRES-Venus This paper N/A pRA1473-CTV-YAP1mut (aa112 S to A) Sivaraj et al.55 N/A pEGFP-Bik Kagawa et al.56 Addgene # 10952 Venus-Bik-4E-pEGFP-C1 Osterlund et al.42 Addgene # 166744 tetO-Bcl2-IRES-tdtomato (TET005) Wu et al.57 Addgene # 117857 Software and algorithms Snap Gene GSL Biotech RRID: SCR_015052 Graphpad Prism GraphPad RRID: SCR_002798 Fiji Schindelin et al.58 RRID: SCR_002285 FlowJo FlowJo RRID: SCR_008520 Seurat Stuart et al.59 RRID:SCR_016341 DESeq2 Liao et al.60 RRID:SCR_015687 UMI-tools Smith et al.61 RRID:SCR_017048 STAR Dobin et al.62 RRID:SCR_004463 Subread Liao et al.63 RRID:SCR_009803 WGCNA Langfelder and Horvath15 RRID:SCR_003302 TopHat2 Kim et al.64 RRID:SCR_013035 HTSeq-count Putri et al.65 RRID:SCR_011867
Western Blot:Article Title: Analyzing embryo dormancy at single-cell resolution reveals dynamic transcriptional responses and activation of integrin-Yap/Taz prosurvival signaling.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Non-essential amino acids Sigma-Aldrich Cat# M7145 Penicillin-streptomycin Sigma-Aldrich Cat# P4333 N2 Thermo Fisher Scientific Cat# 17502048 B27 without vitamin A Thermo Fisher Scientific Cat# 12587001 Trypsin-EDTA (0.25%) Sigma-Aldrich Cat# 25200056 2-mercaptoethanol Sigma-Aldrich Cat# M7522 Formaldehyde (w/v), methanol-free 16% Thermo Fisher Cat# 28908 Triton X-100 Sigma-Aldrich Cat# T9284 PBS without Ca/Mg Sigma-Aldrich Cat# D8537 iTag SYBR green supermix Bio-Rad Cat# 1725120 GoTaq green master mix Promega Cat# M7123 Precision Plus Protein Kaleidoscope protein standard Bio-Rad Cat# 161-0375 PD0325901 Cayman Chemical Cat# 13034 CHIR99021 Tocris Cat# 4423 human Lif homemade A kind gift from Prof. Hans R. Schöler, Max Planck Institute for Molecular Biomedicine, M€unster, Germany Lipophectamine 2000 Thermo Fisher Scientific Cat# 11668027 Doxycyclin Sigma-Aldrich Cat# D9891 4-hydroxytamoxifen (4-OHT) Sigma-Aldrich Cat# H7904 Neomycin Sigma-Aldrich Cat# G8168 Gelatin solution Sigma-Aldrich Cat# 1393 ECL Western Blotting Detection Reagent GE Healthcare Cat# RPN2109 ECL Prime Western Blotting Detection Reagent GE Healthcare Cat# RPN2232 PVDF membrane Millipore Cat# IPVH00010 Mineral oil, embryo-tested Sigma-Aldrich Cat# M5310 PMSF Sigma-Aldrich Cat# P7626 Donkey serum VMR Cat# S2170 PMSG Ceva N/A HCG Ceva N/A Depo Clinovir Pfizer N/A b-estradiol Sigma-Aldrich E8875 M2 medium Sigma-Aldrich Cat# M7167 KSOM Millipore Cat# MR-020P-5F Tamoxifen Sigma-Aldrich Cat# T5648 DMSO Carl Roth Cat# A994.1 Tween 20 Sigma-Aldrich Cat# P7949 Corn oil Sigma-Aldrich Cat# C8267 Tyrode’s solution, Acidic Sigma-Aldrich Cat# T1788 TrypLE Express Enzyme Thermo Fisher Scientific Cat# 12604013 Methanol anhydrous 99.8% Sigma-Aldrich Cat# 322415-100ML Benzyl Alcohol Sigma-Aldrich Cat# 24122-2.5L-M Benzyl Benzoate 99+% Thermo Fisher Scientific Cat# 105860010 Heparin sodium salt Sigma-Aldrich Cat# 3149 Glycine Sigma-Aldrich Cat# G7126 Sodium deoxycholate Sigma-Aldrich Cat# 30970 Critical commercial assays In-Fusion HD cloning kit Clontech Cat# 638909 m-Slide 8 Well Ibidi Cat# 80826 (Continued on next page) e2 Cell Stem Cell 31, 1–18.e1–e8, September 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides see Table S4 N/A Recombinant DNA PyCAG-PBase Wang et al.53 N/A pPB-CAG-rtTAM2-IN Adachi et al.54 N/A pPB-CAG-CreERT2-IRES-Neo Adachi et al.54 N/A pPB-hCMV1-Bik-IRES-Venus This paper N/A pPB-hCMV1-mutBik-IRES-Venus This paper N/A pPB-hCMV1-Bcl2-IRES-Venus This paper N/A pPB-CAG-HA-IRES-Venus This paper N/A pPB-CAG-mYap mut aa112 S to A-IRES-Venus This paper N/A pRA1473-CTV-YAP1mut (aa112 S to A) Sivaraj et al.55 N/A pEGFP-Bik Kagawa et al.56 Addgene # 10952 Venus-Bik-4E-pEGFP-C1 Osterlund et al.42 Addgene # 166744 tetO-Bcl2-IRES-tdtomato (TET005) Wu et al.57 Addgene # 117857 Software and algorithms Snap Gene GSL Biotech RRID: SCR_015052 Graphpad Prism GraphPad RRID: SCR_002798 Fiji Schindelin et al.58 RRID: SCR_002285 FlowJo FlowJo RRID: SCR_008520 Seurat Stuart et al.59 RRID:SCR_016341 DESeq2 Liao et al.60 RRID:SCR_015687 UMI-tools Smith et al.61 RRID:SCR_017048 STAR Dobin et al.62 RRID:SCR_004463 Subread Liao et al.63 RRID:SCR_009803 WGCNA Langfelder and Horvath15 RRID:SCR_003302 TopHat2 Kim et al.64 RRID:SCR_013035 HTSeq-count Putri et al.65 RRID:SCR_011867
Membrane:Article Title: Analyzing embryo dormancy at single-cell resolution reveals dynamic transcriptional responses and activation of integrin-Yap/Taz prosurvival signaling.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Non-essential amino acids Sigma-Aldrich Cat# M7145 Penicillin-streptomycin Sigma-Aldrich Cat# P4333 N2 Thermo Fisher Scientific Cat# 17502048 B27 without vitamin A Thermo Fisher Scientific Cat# 12587001 Trypsin-EDTA (0.25%) Sigma-Aldrich Cat# 25200056 2-mercaptoethanol Sigma-Aldrich Cat# M7522 Formaldehyde (w/v), methanol-free 16% Thermo Fisher Cat# 28908 Triton X-100 Sigma-Aldrich Cat# T9284 PBS without Ca/Mg Sigma-Aldrich Cat# D8537 iTag SYBR green supermix Bio-Rad Cat# 1725120 GoTaq green master mix Promega Cat# M7123 Precision Plus Protein Kaleidoscope protein standard Bio-Rad Cat# 161-0375 PD0325901 Cayman Chemical Cat# 13034 CHIR99021 Tocris Cat# 4423 human Lif homemade A kind gift from Prof. Hans R. Schöler, Max Planck Institute for Molecular Biomedicine, M€unster, Germany Lipophectamine 2000 Thermo Fisher Scientific Cat# 11668027 Doxycyclin Sigma-Aldrich Cat# D9891 4-hydroxytamoxifen (4-OHT) Sigma-Aldrich Cat# H7904 Neomycin Sigma-Aldrich Cat# G8168 Gelatin solution Sigma-Aldrich Cat# 1393 ECL Western Blotting Detection Reagent GE Healthcare Cat# RPN2109 ECL Prime Western Blotting Detection Reagent GE Healthcare Cat# RPN2232 PVDF membrane Millipore Cat# IPVH00010 Mineral oil, embryo-tested Sigma-Aldrich Cat# M5310 PMSF Sigma-Aldrich Cat# P7626 Donkey serum VMR Cat# S2170 PMSG Ceva N/A HCG Ceva N/A Depo Clinovir Pfizer N/A b-estradiol Sigma-Aldrich E8875 M2 medium Sigma-Aldrich Cat# M7167 KSOM Millipore Cat# MR-020P-5F Tamoxifen Sigma-Aldrich Cat# T5648 DMSO Carl Roth Cat# A994.1 Tween 20 Sigma-Aldrich Cat# P7949 Corn oil Sigma-Aldrich Cat# C8267 Tyrode’s solution, Acidic Sigma-Aldrich Cat# T1788 TrypLE Express Enzyme Thermo Fisher Scientific Cat# 12604013 Methanol anhydrous 99.8% Sigma-Aldrich Cat# 322415-100ML Benzyl Alcohol Sigma-Aldrich Cat# 24122-2.5L-M Benzyl Benzoate 99+% Thermo Fisher Scientific Cat# 105860010 Heparin sodium salt Sigma-Aldrich Cat# 3149 Glycine Sigma-Aldrich Cat# G7126 Sodium deoxycholate Sigma-Aldrich Cat# 30970 Critical commercial assays In-Fusion HD cloning kit Clontech Cat# 638909 m-Slide 8 Well Ibidi Cat# 80826 (Continued on next page) e2 Cell Stem Cell 31, 1–18.e1–e8, September 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides see Table S4 N/A Recombinant DNA PyCAG-PBase Wang et al.53 N/A pPB-CAG-rtTAM2-IN Adachi et al.54 N/A pPB-CAG-CreERT2-IRES-Neo Adachi et al.54 N/A pPB-hCMV1-Bik-IRES-Venus This paper N/A pPB-hCMV1-mutBik-IRES-Venus This paper N/A pPB-hCMV1-Bcl2-IRES-Venus This paper N/A pPB-CAG-HA-IRES-Venus This paper N/A pPB-CAG-mYap mut aa112 S to A-IRES-Venus This paper N/A pRA1473-CTV-YAP1mut (aa112 S to A) Sivaraj et al.55 N/A pEGFP-Bik Kagawa et al.56 Addgene # 10952 Venus-Bik-4E-pEGFP-C1 Osterlund et al.42 Addgene # 166744 tetO-Bcl2-IRES-tdtomato (TET005) Wu et al.57 Addgene # 117857 Software and algorithms Snap Gene GSL Biotech RRID: SCR_015052 Graphpad Prism GraphPad RRID: SCR_002798 Fiji Schindelin et al.58 RRID: SCR_002285 FlowJo FlowJo RRID: SCR_008520 Seurat Stuart et al.59 RRID:SCR_016341 DESeq2 Liao et al.60 RRID:SCR_015687 UMI-tools Smith et al.61 RRID:SCR_017048 STAR Dobin et al.62 RRID:SCR_004463 Subread Liao et al.63 RRID:SCR_009803 WGCNA Langfelder and Horvath15 RRID:SCR_003302 TopHat2 Kim et al.64 RRID:SCR_013035 HTSeq-count Putri et al.65 RRID:SCR_011867
Cloning:Article Title: Analyzing embryo dormancy at single-cell resolution reveals dynamic transcriptional responses and activation of integrin-Yap/Taz prosurvival signaling.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Non-essential amino acids Sigma-Aldrich Cat# M7145 Penicillin-streptomycin Sigma-Aldrich Cat# P4333 N2 Thermo Fisher Scientific Cat# 17502048 B27 without vitamin A Thermo Fisher Scientific Cat# 12587001 Trypsin-EDTA (0.25%) Sigma-Aldrich Cat# 25200056 2-mercaptoethanol Sigma-Aldrich Cat# M7522 Formaldehyde (w/v), methanol-free 16% Thermo Fisher Cat# 28908 Triton X-100 Sigma-Aldrich Cat# T9284 PBS without Ca/Mg Sigma-Aldrich Cat# D8537 iTag SYBR green supermix Bio-Rad Cat# 1725120 GoTaq green master mix Promega Cat# M7123 Precision Plus Protein Kaleidoscope protein standard Bio-Rad Cat# 161-0375 PD0325901 Cayman Chemical Cat# 13034 CHIR99021 Tocris Cat# 4423 human Lif homemade A kind gift from Prof. Hans R. Schöler, Max Planck Institute for Molecular Biomedicine, M€unster, Germany Lipophectamine 2000 Thermo Fisher Scientific Cat# 11668027 Doxycyclin Sigma-Aldrich Cat# D9891 4-hydroxytamoxifen (4-OHT) Sigma-Aldrich Cat# H7904 Neomycin Sigma-Aldrich Cat# G8168 Gelatin solution Sigma-Aldrich Cat# 1393 ECL Western Blotting Detection Reagent GE Healthcare Cat# RPN2109 ECL Prime Western Blotting Detection Reagent GE Healthcare Cat# RPN2232 PVDF membrane Millipore Cat# IPVH00010 Mineral oil, embryo-tested Sigma-Aldrich Cat# M5310 PMSF Sigma-Aldrich Cat# P7626 Donkey serum VMR Cat# S2170 PMSG Ceva N/A HCG Ceva N/A Depo Clinovir Pfizer N/A b-estradiol Sigma-Aldrich E8875 M2 medium Sigma-Aldrich Cat# M7167 KSOM Millipore Cat# MR-020P-5F Tamoxifen Sigma-Aldrich Cat# T5648 DMSO Carl Roth Cat# A994.1 Tween 20 Sigma-Aldrich Cat# P7949 Corn oil Sigma-Aldrich Cat# C8267 Tyrode’s solution, Acidic Sigma-Aldrich Cat# T1788 TrypLE Express Enzyme Thermo Fisher Scientific Cat# 12604013 Methanol anhydrous 99.8% Sigma-Aldrich Cat# 322415-100ML Benzyl Alcohol Sigma-Aldrich Cat# 24122-2.5L-M Benzyl Benzoate 99+% Thermo Fisher Scientific Cat# 105860010 Heparin sodium salt Sigma-Aldrich Cat# 3149 Glycine Sigma-Aldrich Cat# G7126 Sodium deoxycholate Sigma-Aldrich Cat# 30970 Critical commercial assays In-Fusion HD cloning kit Clontech Cat# 638909 m-Slide 8 Well Ibidi Cat# 80826 (Continued on next page) e2 Cell Stem Cell 31, 1–18.e1–e8, September 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides see Table S4 N/A Recombinant DNA PyCAG-PBase Wang et al.53 N/A pPB-CAG-rtTAM2-IN Adachi et al.54 N/A pPB-CAG-CreERT2-IRES-Neo Adachi et al.54 N/A pPB-hCMV1-Bik-IRES-Venus This paper N/A pPB-hCMV1-mutBik-IRES-Venus This paper N/A pPB-hCMV1-Bcl2-IRES-Venus This paper N/A pPB-CAG-HA-IRES-Venus This paper N/A pPB-CAG-mYap mut aa112 S to A-IRES-Venus This paper N/A pRA1473-CTV-YAP1mut (aa112 S to A) Sivaraj et al.55 N/A pEGFP-Bik Kagawa et al.56 Addgene # 10952 Venus-Bik-4E-pEGFP-C1 Osterlund et al.42 Addgene # 166744 tetO-Bcl2-IRES-tdtomato (TET005) Wu et al.57 Addgene # 117857 Software and algorithms Snap Gene GSL Biotech RRID: SCR_015052 Graphpad Prism GraphPad RRID: SCR_002798 Fiji Schindelin et al.58 RRID: SCR_002285 FlowJo FlowJo RRID: SCR_008520 Seurat Stuart et al.59 RRID:SCR_016341 DESeq2 Liao et al.60 RRID:SCR_015687 UMI-tools Smith et al.61 RRID:SCR_017048 STAR Dobin et al.62 RRID:SCR_004463 Subread Liao et al.63 RRID:SCR_009803 WGCNA Langfelder and Horvath15 RRID:SCR_003302 TopHat2 Kim et al.64 RRID:SCR_013035 HTSeq-count Putri et al.65 RRID:SCR_011867
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