other:Article Title: Discovery of cytosine deaminases enables base-resolution methylome mapping using a single enzyme.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains dam-/dcm- Competent E. coli NEB Cat# C2925H T7 Express Competent E. coli NEB Cat# C2566H Biological samples GM12878 genomic DNA Coriell Institute NA12878 Single Donor Human Plasma Innovative Research IPLASK2E2ML Unmethylated Lambda DNA Promega D1521 FX174 Virion DNA NEB Cat# N3023S FX174 RF I DNA NEB Cat# N3021S pUC19 Vector NEB Cat# N3041S CpG methylated pUC19 DNA This paper N/A XP-12 phage DNA This paper N/A 1781 bp PCR fragment amplified with dhmCTP This paper N/A T4147 phage DNA Vilnius University Life Sciences Centre N/A T4 AGT- phage DNA Vilnius University Life Sciences Centre N/A PRSSM1.PleII plasmid DNA This paper N/A Isotope-labeled firefly luciferase (Fluc) mRNA This paper N/A Chemicals, peptides, and recombinant proteins CpG Methyltransferase (M.SssI) NEB Cat# M0226S Adenosine 5’-triphosphate (ATP), ammonium salt Cambridge Isotope Laboratories Cat# NLM-3987-CA Cytidine 5’-triphosphate, ammonium salt Cambridge Isotope Laboratories Cat# CNLM-4267-CA-20 Nuclease-free Water NEB Cat# B1500S Bis-Tris Buffer 1M, pH 6.0, Sterile bioWorld Cat# 40120735-1 Triton X-100 Sigma-Aldrich Cat# 11332481001 Thermolabile Proteinase K NEB Cat# P8111S RNase Inhibitor, Murine NEB Cat# M0314S Critical commercial assays NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat# E7645S PURExpress D (aa, tRNA) Kit E6840S NEB Cat# E6840S PURExpress In Vitro Protein Synthesis Kit NEB Cat# E6800S Monarch Plasmid Miniprep Kit NEB Cat# T1010S Monarch Genomic DNA Purification Kit NEB Cat# T3010S Monarch PCR & DNA Cleanup Kit NEB Cat# T1030S NEBNext Q5U Master Mix NEB Cat# M0597S Phusion Hot Start Flex 2X Master Mix NEB Cat# M0536S Nucleoside Digestion Mix NEB Cat# M0649S HiScribe T7 High Yield RNA Synthesis Kit NEB Cat# E2040S Monarch RNA Cleanup Kit NEB Cat# T2040S Qubit RNA broad range assay Thermo Fisher Scientific Cat# Q10211 MAX V2 Cell-Free DNA Extraction Kit BioChain Cat# K5011625MA-V2 (Continued on next page) Molecular Cell 84, 854–866.e1–e7, March 7, 2024 e1
Virus:Article Title: Design of an intracellular aptamer-based fluorescent biosensor to track burden in Escherichia coli.
Article Snippet: .. Key Resources Table REAGENT or RESOURCE SOURCE Trends in Biotechnology, M IDENTIFIER Bacterial and virus strains DH10β NEB # C3019 BL21(DE3) NEB # C2527 Biological samples PURExpress® In Vitro Protein Synthesis Kit NEB # E6800 E. coli S30 Extract System for Circular DNA Promega # L1020 Murine RNase inhibitor NEB # M0314 Chemicals, peptides, and recombinant proteins Chloramphenicol Merck # C1919 Ampicillin Merck # A0166 DFHBI-1T SLS # SML2697-5MG HBC530 Tocris Bioscience # 7277/60U IPTG Merck # I6758 Arabinose Merck # A91906-25G-A HSL Merck # K3007 L-Rhamnose Fluorochem # F492388-25G X-Gal Thermo Fisher # R0404 Oligonucleotides Ultramers IDT N/A Recombinant DNA T7 fluorogenic RNA aptamer library This study N/A J23118 fluorogenic RNA aptamer library This study N/A pBADwt fluorogenic RNA aptamer library This study N/A pBADmut fluorogenic RNA aptamer library This study N/A Htpg1 fluorogenic RNA aptamer library This study N/A M2-VioB-mCherry Ceroni et al 2015 [3] N/A M3-VioB-mCherry Ceroni et al 2015 [3] N/A M4-VioB-mCherry Ceroni et al 2015 [3] N/A pRHA-LacZ Ceroni et al 2018 [19] N/A Software and algorithms FlowJo v10 BD https://www.flowjo.com/ Other Tecan - Infinite M Nano + Monochromator SLS # MIC9266 ClarioSTAR plate reader BMG Labtech Attune CytPix Flow Cytometer Invitrogen Eclipse Ti2-E inverted microscope Nikon onth 2025, Vol. xx, No. xx 17 Experimental model and study participants details Bacterial strains E. coli strains DH10β (K-12 F- λ- araD139 Δ(araA-leu)7697 Δ(lac)X74 galE15 galK16 galU hsdR2 relA rpsL150(StrR) spoT1 deoR φ80dlacZΔM15 endA1 nupG recA1 e14- mcrA Δ(mrr hsdRMS mcrBC)) and BL21(DE3) (F−ompT gal dcm lon hsdSB(rB−mB−) λ(DE3 [lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB+]K-12(λS)) were used. ..
In Vitro:Article Title: Design of an intracellular aptamer-based fluorescent biosensor to track burden in Escherichia coli.
Article Snippet: .. Key Resources Table REAGENT or RESOURCE SOURCE Trends in Biotechnology, M IDENTIFIER Bacterial and virus strains DH10β NEB # C3019 BL21(DE3) NEB # C2527 Biological samples PURExpress® In Vitro Protein Synthesis Kit NEB # E6800 E. coli S30 Extract System for Circular DNA Promega # L1020 Murine RNase inhibitor NEB # M0314 Chemicals, peptides, and recombinant proteins Chloramphenicol Merck # C1919 Ampicillin Merck # A0166 DFHBI-1T SLS # SML2697-5MG HBC530 Tocris Bioscience # 7277/60U IPTG Merck # I6758 Arabinose Merck # A91906-25G-A HSL Merck # K3007 L-Rhamnose Fluorochem # F492388-25G X-Gal Thermo Fisher # R0404 Oligonucleotides Ultramers IDT N/A Recombinant DNA T7 fluorogenic RNA aptamer library This study N/A J23118 fluorogenic RNA aptamer library This study N/A pBADwt fluorogenic RNA aptamer library This study N/A pBADmut fluorogenic RNA aptamer library This study N/A Htpg1 fluorogenic RNA aptamer library This study N/A M2-VioB-mCherry Ceroni et al 2015 [3] N/A M3-VioB-mCherry Ceroni et al 2015 [3] N/A M4-VioB-mCherry Ceroni et al 2015 [3] N/A pRHA-LacZ Ceroni et al 2018 [19] N/A Software and algorithms FlowJo v10 BD https://www.flowjo.com/ Other Tecan - Infinite M Nano + Monochromator SLS # MIC9266 ClarioSTAR plate reader BMG Labtech Attune CytPix Flow Cytometer Invitrogen Eclipse Ti2-E inverted microscope Nikon onth 2025, Vol. xx, No. xx 17 Experimental model and study participants details Bacterial strains E. coli strains DH10β (K-12 F- λ- araD139 Δ(araA-leu)7697 Δ(lac)X74 galE15 galK16 galU hsdR2 relA rpsL150(StrR) spoT1 deoR φ80dlacZΔM15 endA1 nupG recA1 e14- mcrA Δ(mrr hsdRMS mcrBC)) and BL21(DE3) (F−ompT gal dcm lon hsdSB(rB−mB−) λ(DE3 [lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB+]K-12(λS)) were used. ..
Article Title: Cell-Free Gene Expression Dynamics in Synthetic Cell Populations
Article Snippet: .. Name Supplier Catalog No. HiScribe T7 High Yield RNA Synthesis Kit NEB, USA E2040 NEBuilder HiFi DNA Assembly Kit NEB, USA E2621 PURExpress In Vitro Protein Synthesis Kit NEB, USA E6800 QIAGEN Plasmid Maxi Kit QIAGEN, Germany 12162 QIAGEN RNeasy Mini kit QIAGEN, Germany 74104 QIAquick Gel Extraction Kit QIAGEN, Germany 28704 QIAquick PCR Purification Kit QIAGEN, Germany 28104 Quick Start Bradford Assay Bio-Rad, USA 5000201 Table S3. ..
Recombinant:Article Title: Design of an intracellular aptamer-based fluorescent biosensor to track burden in Escherichia coli.
Article Snippet: .. Key Resources Table REAGENT or RESOURCE SOURCE Trends in Biotechnology, M IDENTIFIER Bacterial and virus strains DH10β NEB # C3019 BL21(DE3) NEB # C2527 Biological samples PURExpress® In Vitro Protein Synthesis Kit NEB # E6800 E. coli S30 Extract System for Circular DNA Promega # L1020 Murine RNase inhibitor NEB # M0314 Chemicals, peptides, and recombinant proteins Chloramphenicol Merck # C1919 Ampicillin Merck # A0166 DFHBI-1T SLS # SML2697-5MG HBC530 Tocris Bioscience # 7277/60U IPTG Merck # I6758 Arabinose Merck # A91906-25G-A HSL Merck # K3007 L-Rhamnose Fluorochem # F492388-25G X-Gal Thermo Fisher # R0404 Oligonucleotides Ultramers IDT N/A Recombinant DNA T7 fluorogenic RNA aptamer library This study N/A J23118 fluorogenic RNA aptamer library This study N/A pBADwt fluorogenic RNA aptamer library This study N/A pBADmut fluorogenic RNA aptamer library This study N/A Htpg1 fluorogenic RNA aptamer library This study N/A M2-VioB-mCherry Ceroni et al 2015 [3] N/A M3-VioB-mCherry Ceroni et al 2015 [3] N/A M4-VioB-mCherry Ceroni et al 2015 [3] N/A pRHA-LacZ Ceroni et al 2018 [19] N/A Software and algorithms FlowJo v10 BD https://www.flowjo.com/ Other Tecan - Infinite M Nano + Monochromator SLS # MIC9266 ClarioSTAR plate reader BMG Labtech Attune CytPix Flow Cytometer Invitrogen Eclipse Ti2-E inverted microscope Nikon onth 2025, Vol. xx, No. xx 17 Experimental model and study participants details Bacterial strains E. coli strains DH10β (K-12 F- λ- araD139 Δ(araA-leu)7697 Δ(lac)X74 galE15 galK16 galU hsdR2 relA rpsL150(StrR) spoT1 deoR φ80dlacZΔM15 endA1 nupG recA1 e14- mcrA Δ(mrr hsdRMS mcrBC)) and BL21(DE3) (F−ompT gal dcm lon hsdSB(rB−mB−) λ(DE3 [lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB+]K-12(λS)) were used. ..
Software:Article Title: Design of an intracellular aptamer-based fluorescent biosensor to track burden in Escherichia coli.
Article Snippet: .. Key Resources Table REAGENT or RESOURCE SOURCE Trends in Biotechnology, M IDENTIFIER Bacterial and virus strains DH10β NEB # C3019 BL21(DE3) NEB # C2527 Biological samples PURExpress® In Vitro Protein Synthesis Kit NEB # E6800 E. coli S30 Extract System for Circular DNA Promega # L1020 Murine RNase inhibitor NEB # M0314 Chemicals, peptides, and recombinant proteins Chloramphenicol Merck # C1919 Ampicillin Merck # A0166 DFHBI-1T SLS # SML2697-5MG HBC530 Tocris Bioscience # 7277/60U IPTG Merck # I6758 Arabinose Merck # A91906-25G-A HSL Merck # K3007 L-Rhamnose Fluorochem # F492388-25G X-Gal Thermo Fisher # R0404 Oligonucleotides Ultramers IDT N/A Recombinant DNA T7 fluorogenic RNA aptamer library This study N/A J23118 fluorogenic RNA aptamer library This study N/A pBADwt fluorogenic RNA aptamer library This study N/A pBADmut fluorogenic RNA aptamer library This study N/A Htpg1 fluorogenic RNA aptamer library This study N/A M2-VioB-mCherry Ceroni et al 2015 [3] N/A M3-VioB-mCherry Ceroni et al 2015 [3] N/A M4-VioB-mCherry Ceroni et al 2015 [3] N/A pRHA-LacZ Ceroni et al 2018 [19] N/A Software and algorithms FlowJo v10 BD https://www.flowjo.com/ Other Tecan - Infinite M Nano + Monochromator SLS # MIC9266 ClarioSTAR plate reader BMG Labtech Attune CytPix Flow Cytometer Invitrogen Eclipse Ti2-E inverted microscope Nikon onth 2025, Vol. xx, No. xx 17 Experimental model and study participants details Bacterial strains E. coli strains DH10β (K-12 F- λ- araD139 Δ(araA-leu)7697 Δ(lac)X74 galE15 galK16 galU hsdR2 relA rpsL150(StrR) spoT1 deoR φ80dlacZΔM15 endA1 nupG recA1 e14- mcrA Δ(mrr hsdRMS mcrBC)) and BL21(DE3) (F−ompT gal dcm lon hsdSB(rB−mB−) λ(DE3 [lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB+]K-12(λS)) were used. ..
Flow Cytometry:Article Title: Design of an intracellular aptamer-based fluorescent biosensor to track burden in Escherichia coli.
Article Snippet: .. Key Resources Table REAGENT or RESOURCE SOURCE Trends in Biotechnology, M IDENTIFIER Bacterial and virus strains DH10β NEB # C3019 BL21(DE3) NEB # C2527 Biological samples PURExpress® In Vitro Protein Synthesis Kit NEB # E6800 E. coli S30 Extract System for Circular DNA Promega # L1020 Murine RNase inhibitor NEB # M0314 Chemicals, peptides, and recombinant proteins Chloramphenicol Merck # C1919 Ampicillin Merck # A0166 DFHBI-1T SLS # SML2697-5MG HBC530 Tocris Bioscience # 7277/60U IPTG Merck # I6758 Arabinose Merck # A91906-25G-A HSL Merck # K3007 L-Rhamnose Fluorochem # F492388-25G X-Gal Thermo Fisher # R0404 Oligonucleotides Ultramers IDT N/A Recombinant DNA T7 fluorogenic RNA aptamer library This study N/A J23118 fluorogenic RNA aptamer library This study N/A pBADwt fluorogenic RNA aptamer library This study N/A pBADmut fluorogenic RNA aptamer library This study N/A Htpg1 fluorogenic RNA aptamer library This study N/A M2-VioB-mCherry Ceroni et al 2015 [3] N/A M3-VioB-mCherry Ceroni et al 2015 [3] N/A M4-VioB-mCherry Ceroni et al 2015 [3] N/A pRHA-LacZ Ceroni et al 2018 [19] N/A Software and algorithms FlowJo v10 BD https://www.flowjo.com/ Other Tecan - Infinite M Nano + Monochromator SLS # MIC9266 ClarioSTAR plate reader BMG Labtech Attune CytPix Flow Cytometer Invitrogen Eclipse Ti2-E inverted microscope Nikon onth 2025, Vol. xx, No. xx 17 Experimental model and study participants details Bacterial strains E. coli strains DH10β (K-12 F- λ- araD139 Δ(araA-leu)7697 Δ(lac)X74 galE15 galK16 galU hsdR2 relA rpsL150(StrR) spoT1 deoR φ80dlacZΔM15 endA1 nupG recA1 e14- mcrA Δ(mrr hsdRMS mcrBC)) and BL21(DE3) (F−ompT gal dcm lon hsdSB(rB−mB−) λ(DE3 [lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB+]K-12(λS)) were used. ..
Inverted Microscopy:Article Title: Design of an intracellular aptamer-based fluorescent biosensor to track burden in Escherichia coli.
Article Snippet: .. Key Resources Table REAGENT or RESOURCE SOURCE Trends in Biotechnology, M IDENTIFIER Bacterial and virus strains DH10β NEB # C3019 BL21(DE3) NEB # C2527 Biological samples PURExpress® In Vitro Protein Synthesis Kit NEB # E6800 E. coli S30 Extract System for Circular DNA Promega # L1020 Murine RNase inhibitor NEB # M0314 Chemicals, peptides, and recombinant proteins Chloramphenicol Merck # C1919 Ampicillin Merck # A0166 DFHBI-1T SLS # SML2697-5MG HBC530 Tocris Bioscience # 7277/60U IPTG Merck # I6758 Arabinose Merck # A91906-25G-A HSL Merck # K3007 L-Rhamnose Fluorochem # F492388-25G X-Gal Thermo Fisher # R0404 Oligonucleotides Ultramers IDT N/A Recombinant DNA T7 fluorogenic RNA aptamer library This study N/A J23118 fluorogenic RNA aptamer library This study N/A pBADwt fluorogenic RNA aptamer library This study N/A pBADmut fluorogenic RNA aptamer library This study N/A Htpg1 fluorogenic RNA aptamer library This study N/A M2-VioB-mCherry Ceroni et al 2015 [3] N/A M3-VioB-mCherry Ceroni et al 2015 [3] N/A M4-VioB-mCherry Ceroni et al 2015 [3] N/A pRHA-LacZ Ceroni et al 2018 [19] N/A Software and algorithms FlowJo v10 BD https://www.flowjo.com/ Other Tecan - Infinite M Nano + Monochromator SLS # MIC9266 ClarioSTAR plate reader BMG Labtech Attune CytPix Flow Cytometer Invitrogen Eclipse Ti2-E inverted microscope Nikon onth 2025, Vol. xx, No. xx 17 Experimental model and study participants details Bacterial strains E. coli strains DH10β (K-12 F- λ- araD139 Δ(araA-leu)7697 Δ(lac)X74 galE15 galK16 galU hsdR2 relA rpsL150(StrR) spoT1 deoR φ80dlacZΔM15 endA1 nupG recA1 e14- mcrA Δ(mrr hsdRMS mcrBC)) and BL21(DE3) (F−ompT gal dcm lon hsdSB(rB−mB−) λ(DE3 [lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB+]K-12(λS)) were used. ..
Plasmid Preparation:Article Title: Cell-Free Gene Expression Dynamics in Synthetic Cell Populations
Article Snippet: .. Name Supplier Catalog No. HiScribe T7 High Yield RNA Synthesis Kit NEB, USA E2040 NEBuilder HiFi DNA Assembly Kit NEB, USA E2621 PURExpress In Vitro Protein Synthesis Kit NEB, USA E6800 QIAGEN Plasmid Maxi Kit QIAGEN, Germany 12162 QIAGEN RNeasy Mini kit QIAGEN, Germany 74104 QIAquick Gel Extraction Kit QIAGEN, Germany 28704 QIAquick PCR Purification Kit QIAGEN, Germany 28104 Quick Start Bradford Assay Bio-Rad, USA 5000201 Table S3. ..
Gel Extraction:Article Title: Cell-Free Gene Expression Dynamics in Synthetic Cell Populations
Article Snippet: .. Name Supplier Catalog No. HiScribe T7 High Yield RNA Synthesis Kit NEB, USA E2040 NEBuilder HiFi DNA Assembly Kit NEB, USA E2621 PURExpress In Vitro Protein Synthesis Kit NEB, USA E6800 QIAGEN Plasmid Maxi Kit QIAGEN, Germany 12162 QIAGEN RNeasy Mini kit QIAGEN, Germany 74104 QIAquick Gel Extraction Kit QIAGEN, Germany 28704 QIAquick PCR Purification Kit QIAGEN, Germany 28104 Quick Start Bradford Assay Bio-Rad, USA 5000201 Table S3. ..
Polymerase Chain Reaction:Article Title: Cell-Free Gene Expression Dynamics in Synthetic Cell Populations
Article Snippet: .. Name Supplier Catalog No. HiScribe T7 High Yield RNA Synthesis Kit NEB, USA E2040 NEBuilder HiFi DNA Assembly Kit NEB, USA E2621 PURExpress In Vitro Protein Synthesis Kit NEB, USA E6800 QIAGEN Plasmid Maxi Kit QIAGEN, Germany 12162 QIAGEN RNeasy Mini kit QIAGEN, Germany 74104 QIAquick Gel Extraction Kit QIAGEN, Germany 28704 QIAquick PCR Purification Kit QIAGEN, Germany 28104 Quick Start Bradford Assay Bio-Rad, USA 5000201 Table S3. ..
Purification:Article Title: Cell-Free Gene Expression Dynamics in Synthetic Cell Populations
Article Snippet: .. Name Supplier Catalog No. HiScribe T7 High Yield RNA Synthesis Kit NEB, USA E2040 NEBuilder HiFi DNA Assembly Kit NEB, USA E2621 PURExpress In Vitro Protein Synthesis Kit NEB, USA E6800 QIAGEN Plasmid Maxi Kit QIAGEN, Germany 12162 QIAGEN RNeasy Mini kit QIAGEN, Germany 74104 QIAquick Gel Extraction Kit QIAGEN, Germany 28704 QIAquick PCR Purification Kit QIAGEN, Germany 28104 Quick Start Bradford Assay Bio-Rad, USA 5000201 Table S3. ..
Bradford Assay:Article Title: Cell-Free Gene Expression Dynamics in Synthetic Cell Populations
Article Snippet: .. Name Supplier Catalog No. HiScribe T7 High Yield RNA Synthesis Kit NEB, USA E2040 NEBuilder HiFi DNA Assembly Kit NEB, USA E2621 PURExpress In Vitro Protein Synthesis Kit NEB, USA E6800 QIAGEN Plasmid Maxi Kit QIAGEN, Germany 12162 QIAGEN RNeasy Mini kit QIAGEN, Germany 74104 QIAquick Gel Extraction Kit QIAGEN, Germany 28704 QIAquick PCR Purification Kit QIAGEN, Germany 28104 Quick Start Bradford Assay Bio-Rad, USA 5000201 Table S3. ..
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