other:Article Title: Generalization of neoantigen-based tumor vaccine by delivering peptide-MHC complex via oncolytic virus.
Article Snippet: Reagents and tools table Reagent/Resource Reference or Source Identifier or Catalog Number Experimental models HEK293T (H. sapiens) ATCC Cat #CRL-3216 HepG2 (H. sapiens) ATCC Cat #HB-8065 SK-Hep-1 (H. sapiens) ATCC Cat #HTB-52 SNU-449 (H. sapiens) ATCC Cat #CRL-2234 T2 (H. sapiens) ATCC Cat #CRL-1992 16 EMBO Molecular Medicine © The Author(s) D ow nloaded from https://w w w .em bopress.org on A pril 10, 2025 from IP 2400:1a00:b030:a677:3cf3:c850:bf8c:800b.
Recombinant:Article Title: UBE2O-mediated ubiquitylation directs cytoplasmic CTNNA1 to promote cell-to-ECM adhesions.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HEK293T (H. sapiens) ATCC CRL-3216TM Expi293F (H. sapiens) Gibco A14527 U-2 OS (H. sapiens) ATCC HTB-96TM MEF (M. musculus) This study N/A MDCK (Canis lupus familiaris) Cell bank of the Chinese Academy of Sciences NBL-2 BL21 (DE3) (E. coli) Zhang et al, 2017 N/A Recombinant DNA pLV-Flag-CTNNA1 This study N/A pCR3.1-Myc-CTNNA1 This study N/A pCR3.1-HA-CTNNA1 This study N/A pGEX-6P-1-CTNNA1-Myc This study N/A pGEX-6P-1-CTNNA1-V5 This study N/A pCR3.1-Myc-CTNNA1 deletions This study N/A Reagent/resource Reference or source Identifier or catalog number pCR3.1-HA-CTNNA1-KR This study N/A pCR3.1-HA-CTNNA1-5KR This study N/A pCR3.1-Myc-CTNNA1-S641A This study N/A pCR3.1-Myc-CTNNA1-S641D This study N/A pCR3.1-HA-CTNNA1-KO This study N/A pLV-Flag-CTNNA1-KO This study N/A pLV-Flag-ResCTNNA1 This study N/A pLV-Flag-ResCTNNA1-KO This study N/A pCR3.1-Flag-CTNNA2 This study N/A pCR3.1-UBE2O-Myc Huang et al, 2022; Zhang et al, 2013b N/A pCR3.1-UBE2O-C1040S-mutated (CS)-Myc Huang et al, 2022; Zhang et al, 2013b N/A pLV-Flag-UBE2O Huang et al, 2022; Zhang et al, 2013b N/A pLV-Flag-UBE2O-CS Huang et al, 2022; Zhang et al, 2013b N/A pLV-Flag-UBE2O deletions Huang et al, 2022; Zhang et al, 2013b N/A pLV-Flag-UBE2O-TwinStrep Huang et al, 2022; Zhang et al, 2013b N/A pCR3.1-6×His-Myc-Ubiquitin Huang et al, 2022 N/A pET28a-His-HA-Ubiquitin This study N/A pET28a-His-HA-Ubiquitin-KO This study N/A pET28a-6×His-mUBA1 This study N/A pLV-GFP-zyxin This study N/A pCDNA3-Flag-CTNNB1 This study N/A Antibodies Goat anti-rabbit secondary HRPconjugated antibody Bethyl Laboratories A120-101P Goat anti-mouse secondary HRPconjugated antibody Bethyl Laboratories A90-116P Rabbit anti-Myc Proteintech 16286-1-AP Rabbit anti-HA Sigma-Aldrich H6908 Mouse anti-Flag tag Sigma-Aldrich F1804 Rabbit anti-Flag Merck Millipore F7425 Rabbit anti-UBE2O Novus NBP1-03336 Rabbit anti-UBE2O Cell Signaling Technology 83393S Rabbit anti-UBE2O Bethyl Laboratories A301-873A Rabbit IgG Bethyl Laboratories P120-101 Rabbit anti-CTNNA1 Proteintech 12831-1-AP Mouse anti-CTNNA1 Abcam ab231306 Mouse anti-streptag II Merck Millipore 71590-3cn Rabbit anti-V5 tag GeneTex GTX117997 Rabbit anti-GFP tag Proteintech 50430-2-AP Mouse anti-β-Actin-HRP Santa Cruz Biotechnology SC-47778 © The Author(s) EMBO reports 13 D ow nloaded from https://w w w .em bopress.org on Septem ber 29, 2025 from IP 182.93.78.163. .. Reagent/resource Reference or source Identifier or catalog number Subcellular Protein Fractionation Kit for Cultured Cells ThermoFisher Scientific 78840 Nitrocellulose membrane Cytiva 10600003 8-cell chamber slides Falcon 354108 24-well Transwell plates Corning 3422 DAPI Cell Signaling Technology 4083S CoraLite®594-Phalloidin Proteintech PF00003 Antifade Mounting Medium Beyotime P0126 Software MaxQuant v1.6.17.0 and v2.0.3.0) Tyanova et al, 2016 Fiji v2.9.0 Schindelin et al, 2012 GraphPad Prism v10.2.3 https://www. graphpad.com DEP2 package Feng et al, 2023; Zhang et al, 2018 Other Plasmids, cell culture and transfection The full-length mouse Ctnna1 was amplified from cDNA of IB10 cells and subsequently cloned into CMV promoter-based Flag-, Myc- or HA-tagged vectors as described before (Zhang et al, 2008; Zhang et al, 2013b).
Article Title: p53 pulse modulation differentially regulates target gene promoters to regulate cell fate decisions.
Article Snippet: .. Reagent/Resource Reference or source Identifier or catalog number Experimental models HEK293T (Homo sapiens) ATCC CRL-1573 MCF-7 (Homo sapiens) ATCC HTB-22 MCF-7 + p53-Venus Batchelor et al (2008) N/A MCF-7 + p53-ECFP + hMDM2 promoter hMDM2 + EYFP Lahav et al (2004) N/A MCF-7 + p53-Venus + CDKN1Ap-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + MDM2p-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + EF1ap-mCherry-Geminin This study N/A Recombinant DNA pEB62 = pRRL-R4R3 + Puromycin selection marker This study N/A pEB67 = pDONRP2RP3 + PEST-SV40 NLS This study N/A pEB100 = pDONR221 + mCherry This study N/A pEB78 = pDONRP4P1R + MDM2 promoter This study N/A pEB237 = pDONRP4P1r + CDKN1A promoter This study N/A pEB330 = pEB62 + MDM2 promoter + mCherry + PEST-NLS This study N/A pEB331 = pEB62 + CDKN1A promoter + mCherry + PEST-NLS This study N/A pLV-EF-mCherry-Geminin IRES-Puro Cappell et al (2016) N/A p273 Loewer et al (2010) N/A pLV-EF1a-IRES-Puro Hayer et al (2016) N/A Antibodies Mouse monoclonal anti-p53 DO-1 antibody Santa Cruz Biotechnology sc-126 Rabbit monoclonal anti-b-actin 13E5 Cell Signaling Technology 4970 Donkey anti-mouse 680RD LI-COR Biosciences 926-68072 Donkey anti-rabbit 800CW LI-COR Biosciences 926-32213 Oligonucleotides PCR primers This study Table EV1 Chemicals, enzymes and other reagents Neocarzinostatin Sigma-Aldrich N9162 Nutlin-3 Sigma-Aldrich N6287 Antibiotic–antimycotic solution Corning 30-004-CI Lipofectamine® 3000 transfection reagent Thermo Fisher L3000-008 M-PER mammalian protein extraction reagent Thermo Fisher 78501 SsoAdvancedTM Universal SYBR® Green Supermix Bio-Rad 172-5270 Phusion® High-Fidelity DNA Polymerase New England Biolabs M0530S Deoxynucleotide (dNTP) Solution Mix New England Biolabs N0447S Software MATLAB2019a Mathworks NIS-Elements Nikon ImageJ Schneider et al, 2012; https://imagej.nih.gov/ij/ Image Studio v3.1 LI-COR Biosciences CellASIC® ONIX2 FG Millipore Sigma 10 of 15 Molecular Systems Biology 15: e8685 | 2019 a 2019 The Authors D ow nloaded from https://w w w .em bopress.org on A ugust 10, 2024 from IP 104.28.213.124. .. Reagents and Tools table (continued) Reagent/Resource Reference or source Identifier or catalog number CopyCaller® Software v2.0 Applied Biosystems Other TiE inverted fluorescence microscope Nikon iXon Ultra 888 EMCCD Camera ANDOR Technology Ltd CellASIC® ONIX2 Microfluidic System EMD Millipore EAR99 CellASIC® ONIX Microfluidic Plates EMD Millipore M04S MultiSite Gateway® Three-Fragment Vector Construction Kit Thermo Fisher 12537023 Custom TaqManTM Copy Number Assay Applied Biosystems 4400294 TaqMan® Copy Number Reference Assay RNaseP Applied Biosystems 4403326 Lenti-XTM Packaging Single Shots Clontech 631275 Lenti-X GoStixTM Clontech 631243
Article Title: Cysteine-reactive covalent chloro-N-acetamide ligands induce ferroptosis mediated cell death.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HEK293T (H. sapiens) ATCC (CRL-3216) RRID: CVCL_0063 HEK293T BRD4-HiBiT (H. sapiens) Gifted by Promega N/A HeLa (H. sapiens) ATCC (CCL-2) RRID: CVCL_0030 HeLa RNF4-Flag (H. sapiens) Provided by J. KeitenSchmitz N/A HeLa RNF4 KO (H. sapiens) Provided by J. KeitenSchmitz N/A HeLa Trex Flp in RNF4 WT (H. sapiens) Provided by J. KeitenSchmitz N/A Reagent/resource Reference or source Identifier or catalog number MV4-11 Cas9 (H. sapiens) Gifted by F. Bassermann N/A NB-4 (H. sapiens) ACC 207 (DSMZ) N/A OCI-AML2 (H. sapiens) Leibniz-Institut DSMZ RRID: CVCL_1619 OCI-AML3 Cas9 (H. sapiens) Gifted by H. Uckelmann N/A Recombinant DNA pCMV HA-ubiquitin (Treier et al, 1994) N/A pCMV His-ubiquitin (Treier et al, 1994) N/A pGEX4-T1 GE-Healthcare 28-9545-49 pGEX4-T1-RNF4 WT This study N/A pGEX4-T1-RNF4 C132/125S This study N/A pGEX4-T1-RNF4 C91S This study N/A pGEX4-T1-RNF4 C51S This study N/A pGEX4-T1-RNF4 C51/91S This study N/A pUSEPR-IS_Improved scaffold (empty) Provided by H. Uckelmann N/A pUSEPR-IS_sgRNA NTC_1 Provided by H. Uckelmann N/A pUSEPR-IS_sgRNA NTC_2 Provided by H. Uckelmann N/A pUSEPR-IS_sgRNA RPA3_1 Provided by H. Uckelmann N/A pUSEPR-IS_sgRNA RPA3_2 Provided by H. Uckelmann N/A pUSEPR-IS_sgRNA RNF4_1 This study N/A pUSEPR-IS_sgRNA RNF4_2 This study N/A pUSEPR-IS_sgRNA RNF4_3 This study N/A Antibodies anti-BRD4 (rabbit), monoclonal, 1:1000 Abcam Cat# ab128874; RRID: AB_11145462 anti-CRBN (rabbit), polyclonal, 1:1000 Invitrogen Cat# PA5-38037; RRID: AB_2554641 anti-Flag (M2) (mouse) 1:1000 Sigma Cat# F1804; RRID: AB_262044 anti-GPX4 (rabbit), monoclonal, 1:1000 Abcam Cat# ab125066; RRID: AB_262044 anti-GST (B14) (mouse), monoclonal, 1:1000 Santa Cruz Cat# sc-138; RRID: AB_627677 anti-His Tag (mouse), monoclonal, 1:1000 Santa Cruz Cat# sc-53073; RRID: AB_783791 anti-HMOX1 (rabbit), polyclonal, 1:1000 Proteintech Cat# 10701-1-AP; RRID: AB_2118685 anti-mouse IgG-IRDye 800CW, polyclonal, 1:10,000 Li-COR Cat# 926-32210; RRID: AB_621842 anti-NRF2 (rabbit), polyclonal, 1:5000 Proteintech Cat# 16396-1-AP; AB_2782956 anti-PRDX1 (rabbit), polyclonal, 1:5000 Proteintech Cat# 15816-1-AP; RRID: AB_2170318 anti-rabbit IgG-IRDye 800CW, polyclonal, 1:10,000 Li-COR Cat# 926-32211; RRID: AB_621843 © The Author(s) EMBO reports 13 D ow nloaded from https://w w w .em bopress.org on O ctober 20, 2025 from IP 2804:1b3:a102:1256:b4c9:7aee:29c1:b90d. .. HeLa (female, ATCC®, CCL-2TM) and HEK293T (female, ATCC® CRL-1573TM), purchased from ATCC, and OCI-AML2 (male, Leibniz-Institut DSMZ) cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Thermo Fisher Scientific) supplemented with 10% fetal calf serum (Thermo Fisher Scientific), 100 U/ml penicillin, and 100 U/ml streptomycin (Thermo Fisher Scientific) at 37 °C and 5% CO2.
Selection:Article Title: p53 pulse modulation differentially regulates target gene promoters to regulate cell fate decisions.
Article Snippet: .. Reagent/Resource Reference or source Identifier or catalog number Experimental models HEK293T (Homo sapiens) ATCC CRL-1573 MCF-7 (Homo sapiens) ATCC HTB-22 MCF-7 + p53-Venus Batchelor et al (2008) N/A MCF-7 + p53-ECFP + hMDM2 promoter hMDM2 + EYFP Lahav et al (2004) N/A MCF-7 + p53-Venus + CDKN1Ap-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + MDM2p-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + EF1ap-mCherry-Geminin This study N/A Recombinant DNA pEB62 = pRRL-R4R3 + Puromycin selection marker This study N/A pEB67 = pDONRP2RP3 + PEST-SV40 NLS This study N/A pEB100 = pDONR221 + mCherry This study N/A pEB78 = pDONRP4P1R + MDM2 promoter This study N/A pEB237 = pDONRP4P1r + CDKN1A promoter This study N/A pEB330 = pEB62 + MDM2 promoter + mCherry + PEST-NLS This study N/A pEB331 = pEB62 + CDKN1A promoter + mCherry + PEST-NLS This study N/A pLV-EF-mCherry-Geminin IRES-Puro Cappell et al (2016) N/A p273 Loewer et al (2010) N/A pLV-EF1a-IRES-Puro Hayer et al (2016) N/A Antibodies Mouse monoclonal anti-p53 DO-1 antibody Santa Cruz Biotechnology sc-126 Rabbit monoclonal anti-b-actin 13E5 Cell Signaling Technology 4970 Donkey anti-mouse 680RD LI-COR Biosciences 926-68072 Donkey anti-rabbit 800CW LI-COR Biosciences 926-32213 Oligonucleotides PCR primers This study Table EV1 Chemicals, enzymes and other reagents Neocarzinostatin Sigma-Aldrich N9162 Nutlin-3 Sigma-Aldrich N6287 Antibiotic–antimycotic solution Corning 30-004-CI Lipofectamine® 3000 transfection reagent Thermo Fisher L3000-008 M-PER mammalian protein extraction reagent Thermo Fisher 78501 SsoAdvancedTM Universal SYBR® Green Supermix Bio-Rad 172-5270 Phusion® High-Fidelity DNA Polymerase New England Biolabs M0530S Deoxynucleotide (dNTP) Solution Mix New England Biolabs N0447S Software MATLAB2019a Mathworks NIS-Elements Nikon ImageJ Schneider et al, 2012; https://imagej.nih.gov/ij/ Image Studio v3.1 LI-COR Biosciences CellASIC® ONIX2 FG Millipore Sigma 10 of 15 Molecular Systems Biology 15: e8685 | 2019 a 2019 The Authors D ow nloaded from https://w w w .em bopress.org on A ugust 10, 2024 from IP 104.28.213.124. .. Reagents and Tools table (continued) Reagent/Resource Reference or source Identifier or catalog number CopyCaller® Software v2.0 Applied Biosystems Other TiE inverted fluorescence microscope Nikon iXon Ultra 888 EMCCD Camera ANDOR Technology Ltd CellASIC® ONIX2 Microfluidic System EMD Millipore EAR99 CellASIC® ONIX Microfluidic Plates EMD Millipore M04S MultiSite Gateway® Three-Fragment Vector Construction Kit Thermo Fisher 12537023 Custom TaqManTM Copy Number Assay Applied Biosystems 4400294 TaqMan® Copy Number Reference Assay RNaseP Applied Biosystems 4403326 Lenti-XTM Packaging Single Shots Clontech 631275 Lenti-X GoStixTM Clontech 631243
Marker:Article Title: p53 pulse modulation differentially regulates target gene promoters to regulate cell fate decisions.
Article Snippet: .. Reagent/Resource Reference or source Identifier or catalog number Experimental models HEK293T (Homo sapiens) ATCC CRL-1573 MCF-7 (Homo sapiens) ATCC HTB-22 MCF-7 + p53-Venus Batchelor et al (2008) N/A MCF-7 + p53-ECFP + hMDM2 promoter hMDM2 + EYFP Lahav et al (2004) N/A MCF-7 + p53-Venus + CDKN1Ap-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + MDM2p-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + EF1ap-mCherry-Geminin This study N/A Recombinant DNA pEB62 = pRRL-R4R3 + Puromycin selection marker This study N/A pEB67 = pDONRP2RP3 + PEST-SV40 NLS This study N/A pEB100 = pDONR221 + mCherry This study N/A pEB78 = pDONRP4P1R + MDM2 promoter This study N/A pEB237 = pDONRP4P1r + CDKN1A promoter This study N/A pEB330 = pEB62 + MDM2 promoter + mCherry + PEST-NLS This study N/A pEB331 = pEB62 + CDKN1A promoter + mCherry + PEST-NLS This study N/A pLV-EF-mCherry-Geminin IRES-Puro Cappell et al (2016) N/A p273 Loewer et al (2010) N/A pLV-EF1a-IRES-Puro Hayer et al (2016) N/A Antibodies Mouse monoclonal anti-p53 DO-1 antibody Santa Cruz Biotechnology sc-126 Rabbit monoclonal anti-b-actin 13E5 Cell Signaling Technology 4970 Donkey anti-mouse 680RD LI-COR Biosciences 926-68072 Donkey anti-rabbit 800CW LI-COR Biosciences 926-32213 Oligonucleotides PCR primers This study Table EV1 Chemicals, enzymes and other reagents Neocarzinostatin Sigma-Aldrich N9162 Nutlin-3 Sigma-Aldrich N6287 Antibiotic–antimycotic solution Corning 30-004-CI Lipofectamine® 3000 transfection reagent Thermo Fisher L3000-008 M-PER mammalian protein extraction reagent Thermo Fisher 78501 SsoAdvancedTM Universal SYBR® Green Supermix Bio-Rad 172-5270 Phusion® High-Fidelity DNA Polymerase New England Biolabs M0530S Deoxynucleotide (dNTP) Solution Mix New England Biolabs N0447S Software MATLAB2019a Mathworks NIS-Elements Nikon ImageJ Schneider et al, 2012; https://imagej.nih.gov/ij/ Image Studio v3.1 LI-COR Biosciences CellASIC® ONIX2 FG Millipore Sigma 10 of 15 Molecular Systems Biology 15: e8685 | 2019 a 2019 The Authors D ow nloaded from https://w w w .em bopress.org on A ugust 10, 2024 from IP 104.28.213.124. .. Reagents and Tools table (continued) Reagent/Resource Reference or source Identifier or catalog number CopyCaller® Software v2.0 Applied Biosystems Other TiE inverted fluorescence microscope Nikon iXon Ultra 888 EMCCD Camera ANDOR Technology Ltd CellASIC® ONIX2 Microfluidic System EMD Millipore EAR99 CellASIC® ONIX Microfluidic Plates EMD Millipore M04S MultiSite Gateway® Three-Fragment Vector Construction Kit Thermo Fisher 12537023 Custom TaqManTM Copy Number Assay Applied Biosystems 4400294 TaqMan® Copy Number Reference Assay RNaseP Applied Biosystems 4403326 Lenti-XTM Packaging Single Shots Clontech 631275 Lenti-X GoStixTM Clontech 631243
Polymerase Chain Reaction:Article Title: p53 pulse modulation differentially regulates target gene promoters to regulate cell fate decisions.
Article Snippet: .. Reagent/Resource Reference or source Identifier or catalog number Experimental models HEK293T (Homo sapiens) ATCC CRL-1573 MCF-7 (Homo sapiens) ATCC HTB-22 MCF-7 + p53-Venus Batchelor et al (2008) N/A MCF-7 + p53-ECFP + hMDM2 promoter hMDM2 + EYFP Lahav et al (2004) N/A MCF-7 + p53-Venus + CDKN1Ap-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + MDM2p-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + EF1ap-mCherry-Geminin This study N/A Recombinant DNA pEB62 = pRRL-R4R3 + Puromycin selection marker This study N/A pEB67 = pDONRP2RP3 + PEST-SV40 NLS This study N/A pEB100 = pDONR221 + mCherry This study N/A pEB78 = pDONRP4P1R + MDM2 promoter This study N/A pEB237 = pDONRP4P1r + CDKN1A promoter This study N/A pEB330 = pEB62 + MDM2 promoter + mCherry + PEST-NLS This study N/A pEB331 = pEB62 + CDKN1A promoter + mCherry + PEST-NLS This study N/A pLV-EF-mCherry-Geminin IRES-Puro Cappell et al (2016) N/A p273 Loewer et al (2010) N/A pLV-EF1a-IRES-Puro Hayer et al (2016) N/A Antibodies Mouse monoclonal anti-p53 DO-1 antibody Santa Cruz Biotechnology sc-126 Rabbit monoclonal anti-b-actin 13E5 Cell Signaling Technology 4970 Donkey anti-mouse 680RD LI-COR Biosciences 926-68072 Donkey anti-rabbit 800CW LI-COR Biosciences 926-32213 Oligonucleotides PCR primers This study Table EV1 Chemicals, enzymes and other reagents Neocarzinostatin Sigma-Aldrich N9162 Nutlin-3 Sigma-Aldrich N6287 Antibiotic–antimycotic solution Corning 30-004-CI Lipofectamine® 3000 transfection reagent Thermo Fisher L3000-008 M-PER mammalian protein extraction reagent Thermo Fisher 78501 SsoAdvancedTM Universal SYBR® Green Supermix Bio-Rad 172-5270 Phusion® High-Fidelity DNA Polymerase New England Biolabs M0530S Deoxynucleotide (dNTP) Solution Mix New England Biolabs N0447S Software MATLAB2019a Mathworks NIS-Elements Nikon ImageJ Schneider et al, 2012; https://imagej.nih.gov/ij/ Image Studio v3.1 LI-COR Biosciences CellASIC® ONIX2 FG Millipore Sigma 10 of 15 Molecular Systems Biology 15: e8685 | 2019 a 2019 The Authors D ow nloaded from https://w w w .em bopress.org on A ugust 10, 2024 from IP 104.28.213.124. .. Reagents and Tools table (continued) Reagent/Resource Reference or source Identifier or catalog number CopyCaller® Software v2.0 Applied Biosystems Other TiE inverted fluorescence microscope Nikon iXon Ultra 888 EMCCD Camera ANDOR Technology Ltd CellASIC® ONIX2 Microfluidic System EMD Millipore EAR99 CellASIC® ONIX Microfluidic Plates EMD Millipore M04S MultiSite Gateway® Three-Fragment Vector Construction Kit Thermo Fisher 12537023 Custom TaqManTM Copy Number Assay Applied Biosystems 4400294 TaqMan® Copy Number Reference Assay RNaseP Applied Biosystems 4403326 Lenti-XTM Packaging Single Shots Clontech 631275 Lenti-X GoStixTM Clontech 631243
Transfection:Article Title: p53 pulse modulation differentially regulates target gene promoters to regulate cell fate decisions.
Article Snippet: .. Reagent/Resource Reference or source Identifier or catalog number Experimental models HEK293T (Homo sapiens) ATCC CRL-1573 MCF-7 (Homo sapiens) ATCC HTB-22 MCF-7 + p53-Venus Batchelor et al (2008) N/A MCF-7 + p53-ECFP + hMDM2 promoter hMDM2 + EYFP Lahav et al (2004) N/A MCF-7 + p53-Venus + CDKN1Ap-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + MDM2p-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + EF1ap-mCherry-Geminin This study N/A Recombinant DNA pEB62 = pRRL-R4R3 + Puromycin selection marker This study N/A pEB67 = pDONRP2RP3 + PEST-SV40 NLS This study N/A pEB100 = pDONR221 + mCherry This study N/A pEB78 = pDONRP4P1R + MDM2 promoter This study N/A pEB237 = pDONRP4P1r + CDKN1A promoter This study N/A pEB330 = pEB62 + MDM2 promoter + mCherry + PEST-NLS This study N/A pEB331 = pEB62 + CDKN1A promoter + mCherry + PEST-NLS This study N/A pLV-EF-mCherry-Geminin IRES-Puro Cappell et al (2016) N/A p273 Loewer et al (2010) N/A pLV-EF1a-IRES-Puro Hayer et al (2016) N/A Antibodies Mouse monoclonal anti-p53 DO-1 antibody Santa Cruz Biotechnology sc-126 Rabbit monoclonal anti-b-actin 13E5 Cell Signaling Technology 4970 Donkey anti-mouse 680RD LI-COR Biosciences 926-68072 Donkey anti-rabbit 800CW LI-COR Biosciences 926-32213 Oligonucleotides PCR primers This study Table EV1 Chemicals, enzymes and other reagents Neocarzinostatin Sigma-Aldrich N9162 Nutlin-3 Sigma-Aldrich N6287 Antibiotic–antimycotic solution Corning 30-004-CI Lipofectamine® 3000 transfection reagent Thermo Fisher L3000-008 M-PER mammalian protein extraction reagent Thermo Fisher 78501 SsoAdvancedTM Universal SYBR® Green Supermix Bio-Rad 172-5270 Phusion® High-Fidelity DNA Polymerase New England Biolabs M0530S Deoxynucleotide (dNTP) Solution Mix New England Biolabs N0447S Software MATLAB2019a Mathworks NIS-Elements Nikon ImageJ Schneider et al, 2012; https://imagej.nih.gov/ij/ Image Studio v3.1 LI-COR Biosciences CellASIC® ONIX2 FG Millipore Sigma 10 of 15 Molecular Systems Biology 15: e8685 | 2019 a 2019 The Authors D ow nloaded from https://w w w .em bopress.org on A ugust 10, 2024 from IP 104.28.213.124. .. Reagents and Tools table (continued) Reagent/Resource Reference or source Identifier or catalog number CopyCaller® Software v2.0 Applied Biosystems Other TiE inverted fluorescence microscope Nikon iXon Ultra 888 EMCCD Camera ANDOR Technology Ltd CellASIC® ONIX2 Microfluidic System EMD Millipore EAR99 CellASIC® ONIX Microfluidic Plates EMD Millipore M04S MultiSite Gateway® Three-Fragment Vector Construction Kit Thermo Fisher 12537023 Custom TaqManTM Copy Number Assay Applied Biosystems 4400294 TaqMan® Copy Number Reference Assay RNaseP Applied Biosystems 4403326 Lenti-XTM Packaging Single Shots Clontech 631275 Lenti-X GoStixTM Clontech 631243
Protein Extraction:Article Title: p53 pulse modulation differentially regulates target gene promoters to regulate cell fate decisions.
Article Snippet: .. Reagent/Resource Reference or source Identifier or catalog number Experimental models HEK293T (Homo sapiens) ATCC CRL-1573 MCF-7 (Homo sapiens) ATCC HTB-22 MCF-7 + p53-Venus Batchelor et al (2008) N/A MCF-7 + p53-ECFP + hMDM2 promoter hMDM2 + EYFP Lahav et al (2004) N/A MCF-7 + p53-Venus + CDKN1Ap-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + MDM2p-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + EF1ap-mCherry-Geminin This study N/A Recombinant DNA pEB62 = pRRL-R4R3 + Puromycin selection marker This study N/A pEB67 = pDONRP2RP3 + PEST-SV40 NLS This study N/A pEB100 = pDONR221 + mCherry This study N/A pEB78 = pDONRP4P1R + MDM2 promoter This study N/A pEB237 = pDONRP4P1r + CDKN1A promoter This study N/A pEB330 = pEB62 + MDM2 promoter + mCherry + PEST-NLS This study N/A pEB331 = pEB62 + CDKN1A promoter + mCherry + PEST-NLS This study N/A pLV-EF-mCherry-Geminin IRES-Puro Cappell et al (2016) N/A p273 Loewer et al (2010) N/A pLV-EF1a-IRES-Puro Hayer et al (2016) N/A Antibodies Mouse monoclonal anti-p53 DO-1 antibody Santa Cruz Biotechnology sc-126 Rabbit monoclonal anti-b-actin 13E5 Cell Signaling Technology 4970 Donkey anti-mouse 680RD LI-COR Biosciences 926-68072 Donkey anti-rabbit 800CW LI-COR Biosciences 926-32213 Oligonucleotides PCR primers This study Table EV1 Chemicals, enzymes and other reagents Neocarzinostatin Sigma-Aldrich N9162 Nutlin-3 Sigma-Aldrich N6287 Antibiotic–antimycotic solution Corning 30-004-CI Lipofectamine® 3000 transfection reagent Thermo Fisher L3000-008 M-PER mammalian protein extraction reagent Thermo Fisher 78501 SsoAdvancedTM Universal SYBR® Green Supermix Bio-Rad 172-5270 Phusion® High-Fidelity DNA Polymerase New England Biolabs M0530S Deoxynucleotide (dNTP) Solution Mix New England Biolabs N0447S Software MATLAB2019a Mathworks NIS-Elements Nikon ImageJ Schneider et al, 2012; https://imagej.nih.gov/ij/ Image Studio v3.1 LI-COR Biosciences CellASIC® ONIX2 FG Millipore Sigma 10 of 15 Molecular Systems Biology 15: e8685 | 2019 a 2019 The Authors D ow nloaded from https://w w w .em bopress.org on A ugust 10, 2024 from IP 104.28.213.124. .. Reagents and Tools table (continued) Reagent/Resource Reference or source Identifier or catalog number CopyCaller® Software v2.0 Applied Biosystems Other TiE inverted fluorescence microscope Nikon iXon Ultra 888 EMCCD Camera ANDOR Technology Ltd CellASIC® ONIX2 Microfluidic System EMD Millipore EAR99 CellASIC® ONIX Microfluidic Plates EMD Millipore M04S MultiSite Gateway® Three-Fragment Vector Construction Kit Thermo Fisher 12537023 Custom TaqManTM Copy Number Assay Applied Biosystems 4400294 TaqMan® Copy Number Reference Assay RNaseP Applied Biosystems 4403326 Lenti-XTM Packaging Single Shots Clontech 631275 Lenti-X GoStixTM Clontech 631243
SYBR Green Assay:Article Title: p53 pulse modulation differentially regulates target gene promoters to regulate cell fate decisions.
Article Snippet: .. Reagent/Resource Reference or source Identifier or catalog number Experimental models HEK293T (Homo sapiens) ATCC CRL-1573 MCF-7 (Homo sapiens) ATCC HTB-22 MCF-7 + p53-Venus Batchelor et al (2008) N/A MCF-7 + p53-ECFP + hMDM2 promoter hMDM2 + EYFP Lahav et al (2004) N/A MCF-7 + p53-Venus + CDKN1Ap-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + MDM2p-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + EF1ap-mCherry-Geminin This study N/A Recombinant DNA pEB62 = pRRL-R4R3 + Puromycin selection marker This study N/A pEB67 = pDONRP2RP3 + PEST-SV40 NLS This study N/A pEB100 = pDONR221 + mCherry This study N/A pEB78 = pDONRP4P1R + MDM2 promoter This study N/A pEB237 = pDONRP4P1r + CDKN1A promoter This study N/A pEB330 = pEB62 + MDM2 promoter + mCherry + PEST-NLS This study N/A pEB331 = pEB62 + CDKN1A promoter + mCherry + PEST-NLS This study N/A pLV-EF-mCherry-Geminin IRES-Puro Cappell et al (2016) N/A p273 Loewer et al (2010) N/A pLV-EF1a-IRES-Puro Hayer et al (2016) N/A Antibodies Mouse monoclonal anti-p53 DO-1 antibody Santa Cruz Biotechnology sc-126 Rabbit monoclonal anti-b-actin 13E5 Cell Signaling Technology 4970 Donkey anti-mouse 680RD LI-COR Biosciences 926-68072 Donkey anti-rabbit 800CW LI-COR Biosciences 926-32213 Oligonucleotides PCR primers This study Table EV1 Chemicals, enzymes and other reagents Neocarzinostatin Sigma-Aldrich N9162 Nutlin-3 Sigma-Aldrich N6287 Antibiotic–antimycotic solution Corning 30-004-CI Lipofectamine® 3000 transfection reagent Thermo Fisher L3000-008 M-PER mammalian protein extraction reagent Thermo Fisher 78501 SsoAdvancedTM Universal SYBR® Green Supermix Bio-Rad 172-5270 Phusion® High-Fidelity DNA Polymerase New England Biolabs M0530S Deoxynucleotide (dNTP) Solution Mix New England Biolabs N0447S Software MATLAB2019a Mathworks NIS-Elements Nikon ImageJ Schneider et al, 2012; https://imagej.nih.gov/ij/ Image Studio v3.1 LI-COR Biosciences CellASIC® ONIX2 FG Millipore Sigma 10 of 15 Molecular Systems Biology 15: e8685 | 2019 a 2019 The Authors D ow nloaded from https://w w w .em bopress.org on A ugust 10, 2024 from IP 104.28.213.124. .. Reagents and Tools table (continued) Reagent/Resource Reference or source Identifier or catalog number CopyCaller® Software v2.0 Applied Biosystems Other TiE inverted fluorescence microscope Nikon iXon Ultra 888 EMCCD Camera ANDOR Technology Ltd CellASIC® ONIX2 Microfluidic System EMD Millipore EAR99 CellASIC® ONIX Microfluidic Plates EMD Millipore M04S MultiSite Gateway® Three-Fragment Vector Construction Kit Thermo Fisher 12537023 Custom TaqManTM Copy Number Assay Applied Biosystems 4400294 TaqMan® Copy Number Reference Assay RNaseP Applied Biosystems 4403326 Lenti-XTM Packaging Single Shots Clontech 631275 Lenti-X GoStixTM Clontech 631243
Software:Article Title: p53 pulse modulation differentially regulates target gene promoters to regulate cell fate decisions.
Article Snippet: .. Reagent/Resource Reference or source Identifier or catalog number Experimental models HEK293T (Homo sapiens) ATCC CRL-1573 MCF-7 (Homo sapiens) ATCC HTB-22 MCF-7 + p53-Venus Batchelor et al (2008) N/A MCF-7 + p53-ECFP + hMDM2 promoter hMDM2 + EYFP Lahav et al (2004) N/A MCF-7 + p53-Venus + CDKN1Ap-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + MDM2p-mCherry-NLS-PEST This study N/A MCF-7 + p53-Venus + EF1ap-mCherry-Geminin This study N/A Recombinant DNA pEB62 = pRRL-R4R3 + Puromycin selection marker This study N/A pEB67 = pDONRP2RP3 + PEST-SV40 NLS This study N/A pEB100 = pDONR221 + mCherry This study N/A pEB78 = pDONRP4P1R + MDM2 promoter This study N/A pEB237 = pDONRP4P1r + CDKN1A promoter This study N/A pEB330 = pEB62 + MDM2 promoter + mCherry + PEST-NLS This study N/A pEB331 = pEB62 + CDKN1A promoter + mCherry + PEST-NLS This study N/A pLV-EF-mCherry-Geminin IRES-Puro Cappell et al (2016) N/A p273 Loewer et al (2010) N/A pLV-EF1a-IRES-Puro Hayer et al (2016) N/A Antibodies Mouse monoclonal anti-p53 DO-1 antibody Santa Cruz Biotechnology sc-126 Rabbit monoclonal anti-b-actin 13E5 Cell Signaling Technology 4970 Donkey anti-mouse 680RD LI-COR Biosciences 926-68072 Donkey anti-rabbit 800CW LI-COR Biosciences 926-32213 Oligonucleotides PCR primers This study Table EV1 Chemicals, enzymes and other reagents Neocarzinostatin Sigma-Aldrich N9162 Nutlin-3 Sigma-Aldrich N6287 Antibiotic–antimycotic solution Corning 30-004-CI Lipofectamine® 3000 transfection reagent Thermo Fisher L3000-008 M-PER mammalian protein extraction reagent Thermo Fisher 78501 SsoAdvancedTM Universal SYBR® Green Supermix Bio-Rad 172-5270 Phusion® High-Fidelity DNA Polymerase New England Biolabs M0530S Deoxynucleotide (dNTP) Solution Mix New England Biolabs N0447S Software MATLAB2019a Mathworks NIS-Elements Nikon ImageJ Schneider et al, 2012; https://imagej.nih.gov/ij/ Image Studio v3.1 LI-COR Biosciences CellASIC® ONIX2 FG Millipore Sigma 10 of 15 Molecular Systems Biology 15: e8685 | 2019 a 2019 The Authors D ow nloaded from https://w w w .em bopress.org on A ugust 10, 2024 from IP 104.28.213.124. .. Reagents and Tools table (continued) Reagent/Resource Reference or source Identifier or catalog number CopyCaller® Software v2.0 Applied Biosystems Other TiE inverted fluorescence microscope Nikon iXon Ultra 888 EMCCD Camera ANDOR Technology Ltd CellASIC® ONIX2 Microfluidic System EMD Millipore EAR99 CellASIC® ONIX Microfluidic Plates EMD Millipore M04S MultiSite Gateway® Three-Fragment Vector Construction Kit Thermo Fisher 12537023 Custom TaqManTM Copy Number Assay Applied Biosystems 4400294 TaqMan® Copy Number Reference Assay RNaseP Applied Biosystems 4403326 Lenti-XTM Packaging Single Shots Clontech 631275 Lenti-X GoStixTM Clontech 631243
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