Quantitative RT-PCR:Article Title: Rif-seq reveals Caulobacter crescentus mRNA decay is globally coordinated with transcription and translation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Trizol Invitrogen Cat#15596018 Sucrose Sigma-Aldrich Cat#S0389-1KG Retapamulin Sigma-Aldrich Cat#SBR00057-50MG Chloramphenicol Sigma-Aldrich Cat#C0378-25G FD EcoR1 Thermo Scientific Cat#FD0274 Nhe1 Thermo Scientific Cat#FD0973 Kanamycin Gibco Cat#11815032 Xylose Sigma Aldrich Cat#X1500-500G T4 DNA ligase Thermo Scientific Cat#EL0011 Phusion DNA Polymease Thermo Scientific Cat#F530L FD Dpn1 Thermo Scientific Cat#ER1701 UltraPure TM Ethidium Bromide, 10 mg/mL Invitrogen Cat#15585011 TriTrack DNA Loading Dye (6×) Thermo Scientific Cat#R1161 Chloroform Fisher scientific Cat#AC423550010 Isopropanol Sigma-Aldrich Cat#67-63-0 Sodium Acetate (3 M), pH 5.5, RNase-free Invitrogen Cat#AM9740 GlycoBlue TM Coprecipitant Invitrogen Cat#AM9515 Ethanol Decon laboratories,inc Cat#2701 Nuclease free distilled water Invitrogen Cat#10977049 Luna® Universal One-Step RT-qPCR Kit NEB Cat#E3005L DEPC water Sigma-Aldrich Cat#693520-1L Tris (1 M), pH 8.0, RNase-free Invitrogen Cat#AM9855G MgCl2 (1 M) Invitrogen Cat#AM9530G Ammonium Chloride (99.5%) Sigma-Aldrich Cat#A9434-1KG Triton X-100 Sigma Aldrich Cat#T87T87-100ML NP-40 Surfact-Amps TM Detergent Solution Thermo Scientific Cat#85124 Magnesium sulfate Sigma-Aldrich Cat#M7506-1KG Ferrous sulfate chelate solution (100×) Sigma-Aldrich Cat#F0518-1L DNase I recombinant, RNase-free Roche Cat#4716728001 Tris (1 M), pH 7.0, RNase-free Invitrogen Cat#AM9851 Invitrogen TM Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9722 T4 PNK Thermo Scientific Cat#EK0031 Glucose (99.5%) Sigma-Aldrich Cat#G8270-1KG Bactopeptone Gibco Cat#211677 Yeast extract Milipore Cat#92144-500G-F Sodium Dodecyl Sulfate (98.5%) Sigma-Aldrich Cat#L3771-500G Glycerol Sigma-Aldrich Cat#56-81-5 BD Difco TM Nutrient Agar Fisher scientific Cat#DF0001-17-0 Thermo Scientific TM GeneRuler 1 kb Plus DNA Ladder, ready-to-use Thermo Scientific Cat#FERSM1334 Luria Broth Base Invitrogen Cat#12795084 GeneJET Gel Extraction Kit Thermo Scientific Cat#K0692 GeneJET Plasmid Miniprep Kit Thermo Scientific Cat#K0503 GeneJET PCR Purification Kit Thermo Scientific Cat#K0702 (Continued on next page) Cell Reports 44, 116691, December 23, 2025 15
Recombinant:Article Title: Rif-seq reveals Caulobacter crescentus mRNA decay is globally coordinated with transcription and translation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Trizol Invitrogen Cat#15596018 Sucrose Sigma-Aldrich Cat#S0389-1KG Retapamulin Sigma-Aldrich Cat#SBR00057-50MG Chloramphenicol Sigma-Aldrich Cat#C0378-25G FD EcoR1 Thermo Scientific Cat#FD0274 Nhe1 Thermo Scientific Cat#FD0973 Kanamycin Gibco Cat#11815032 Xylose Sigma Aldrich Cat#X1500-500G T4 DNA ligase Thermo Scientific Cat#EL0011 Phusion DNA Polymease Thermo Scientific Cat#F530L FD Dpn1 Thermo Scientific Cat#ER1701 UltraPure TM Ethidium Bromide, 10 mg/mL Invitrogen Cat#15585011 TriTrack DNA Loading Dye (6×) Thermo Scientific Cat#R1161 Chloroform Fisher scientific Cat#AC423550010 Isopropanol Sigma-Aldrich Cat#67-63-0 Sodium Acetate (3 M), pH 5.5, RNase-free Invitrogen Cat#AM9740 GlycoBlue TM Coprecipitant Invitrogen Cat#AM9515 Ethanol Decon laboratories,inc Cat#2701 Nuclease free distilled water Invitrogen Cat#10977049 Luna® Universal One-Step RT-qPCR Kit NEB Cat#E3005L DEPC water Sigma-Aldrich Cat#693520-1L Tris (1 M), pH 8.0, RNase-free Invitrogen Cat#AM9855G MgCl2 (1 M) Invitrogen Cat#AM9530G Ammonium Chloride (99.5%) Sigma-Aldrich Cat#A9434-1KG Triton X-100 Sigma Aldrich Cat#T87T87-100ML NP-40 Surfact-Amps TM Detergent Solution Thermo Scientific Cat#85124 Magnesium sulfate Sigma-Aldrich Cat#M7506-1KG Ferrous sulfate chelate solution (100×) Sigma-Aldrich Cat#F0518-1L DNase I recombinant, RNase-free Roche Cat#4716728001 Tris (1 M), pH 7.0, RNase-free Invitrogen Cat#AM9851 Invitrogen TM Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9722 T4 PNK Thermo Scientific Cat#EK0031 Glucose (99.5%) Sigma-Aldrich Cat#G8270-1KG Bactopeptone Gibco Cat#211677 Yeast extract Milipore Cat#92144-500G-F Sodium Dodecyl Sulfate (98.5%) Sigma-Aldrich Cat#L3771-500G Glycerol Sigma-Aldrich Cat#56-81-5 BD Difco TM Nutrient Agar Fisher scientific Cat#DF0001-17-0 Thermo Scientific TM GeneRuler 1 kb Plus DNA Ladder, ready-to-use Thermo Scientific Cat#FERSM1334 Luria Broth Base Invitrogen Cat#12795084 GeneJET Gel Extraction Kit Thermo Scientific Cat#K0692 GeneJET Plasmid Miniprep Kit Thermo Scientific Cat#K0503 GeneJET PCR Purification Kit Thermo Scientific Cat#K0702 (Continued on next page) Cell Reports 44, 116691, December 23, 2025 15
Gel Extraction:Article Title: Rif-seq reveals Caulobacter crescentus mRNA decay is globally coordinated with transcription and translation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Trizol Invitrogen Cat#15596018 Sucrose Sigma-Aldrich Cat#S0389-1KG Retapamulin Sigma-Aldrich Cat#SBR00057-50MG Chloramphenicol Sigma-Aldrich Cat#C0378-25G FD EcoR1 Thermo Scientific Cat#FD0274 Nhe1 Thermo Scientific Cat#FD0973 Kanamycin Gibco Cat#11815032 Xylose Sigma Aldrich Cat#X1500-500G T4 DNA ligase Thermo Scientific Cat#EL0011 Phusion DNA Polymease Thermo Scientific Cat#F530L FD Dpn1 Thermo Scientific Cat#ER1701 UltraPure TM Ethidium Bromide, 10 mg/mL Invitrogen Cat#15585011 TriTrack DNA Loading Dye (6×) Thermo Scientific Cat#R1161 Chloroform Fisher scientific Cat#AC423550010 Isopropanol Sigma-Aldrich Cat#67-63-0 Sodium Acetate (3 M), pH 5.5, RNase-free Invitrogen Cat#AM9740 GlycoBlue TM Coprecipitant Invitrogen Cat#AM9515 Ethanol Decon laboratories,inc Cat#2701 Nuclease free distilled water Invitrogen Cat#10977049 Luna® Universal One-Step RT-qPCR Kit NEB Cat#E3005L DEPC water Sigma-Aldrich Cat#693520-1L Tris (1 M), pH 8.0, RNase-free Invitrogen Cat#AM9855G MgCl2 (1 M) Invitrogen Cat#AM9530G Ammonium Chloride (99.5%) Sigma-Aldrich Cat#A9434-1KG Triton X-100 Sigma Aldrich Cat#T87T87-100ML NP-40 Surfact-Amps TM Detergent Solution Thermo Scientific Cat#85124 Magnesium sulfate Sigma-Aldrich Cat#M7506-1KG Ferrous sulfate chelate solution (100×) Sigma-Aldrich Cat#F0518-1L DNase I recombinant, RNase-free Roche Cat#4716728001 Tris (1 M), pH 7.0, RNase-free Invitrogen Cat#AM9851 Invitrogen TM Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9722 T4 PNK Thermo Scientific Cat#EK0031 Glucose (99.5%) Sigma-Aldrich Cat#G8270-1KG Bactopeptone Gibco Cat#211677 Yeast extract Milipore Cat#92144-500G-F Sodium Dodecyl Sulfate (98.5%) Sigma-Aldrich Cat#L3771-500G Glycerol Sigma-Aldrich Cat#56-81-5 BD Difco TM Nutrient Agar Fisher scientific Cat#DF0001-17-0 Thermo Scientific TM GeneRuler 1 kb Plus DNA Ladder, ready-to-use Thermo Scientific Cat#FERSM1334 Luria Broth Base Invitrogen Cat#12795084 GeneJET Gel Extraction Kit Thermo Scientific Cat#K0692 GeneJET Plasmid Miniprep Kit Thermo Scientific Cat#K0503 GeneJET PCR Purification Kit Thermo Scientific Cat#K0702 (Continued on next page) Cell Reports 44, 116691, December 23, 2025 15
Plasmid Preparation:Article Title: Rif-seq reveals Caulobacter crescentus mRNA decay is globally coordinated with transcription and translation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Trizol Invitrogen Cat#15596018 Sucrose Sigma-Aldrich Cat#S0389-1KG Retapamulin Sigma-Aldrich Cat#SBR00057-50MG Chloramphenicol Sigma-Aldrich Cat#C0378-25G FD EcoR1 Thermo Scientific Cat#FD0274 Nhe1 Thermo Scientific Cat#FD0973 Kanamycin Gibco Cat#11815032 Xylose Sigma Aldrich Cat#X1500-500G T4 DNA ligase Thermo Scientific Cat#EL0011 Phusion DNA Polymease Thermo Scientific Cat#F530L FD Dpn1 Thermo Scientific Cat#ER1701 UltraPure TM Ethidium Bromide, 10 mg/mL Invitrogen Cat#15585011 TriTrack DNA Loading Dye (6×) Thermo Scientific Cat#R1161 Chloroform Fisher scientific Cat#AC423550010 Isopropanol Sigma-Aldrich Cat#67-63-0 Sodium Acetate (3 M), pH 5.5, RNase-free Invitrogen Cat#AM9740 GlycoBlue TM Coprecipitant Invitrogen Cat#AM9515 Ethanol Decon laboratories,inc Cat#2701 Nuclease free distilled water Invitrogen Cat#10977049 Luna® Universal One-Step RT-qPCR Kit NEB Cat#E3005L DEPC water Sigma-Aldrich Cat#693520-1L Tris (1 M), pH 8.0, RNase-free Invitrogen Cat#AM9855G MgCl2 (1 M) Invitrogen Cat#AM9530G Ammonium Chloride (99.5%) Sigma-Aldrich Cat#A9434-1KG Triton X-100 Sigma Aldrich Cat#T87T87-100ML NP-40 Surfact-Amps TM Detergent Solution Thermo Scientific Cat#85124 Magnesium sulfate Sigma-Aldrich Cat#M7506-1KG Ferrous sulfate chelate solution (100×) Sigma-Aldrich Cat#F0518-1L DNase I recombinant, RNase-free Roche Cat#4716728001 Tris (1 M), pH 7.0, RNase-free Invitrogen Cat#AM9851 Invitrogen TM Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9722 T4 PNK Thermo Scientific Cat#EK0031 Glucose (99.5%) Sigma-Aldrich Cat#G8270-1KG Bactopeptone Gibco Cat#211677 Yeast extract Milipore Cat#92144-500G-F Sodium Dodecyl Sulfate (98.5%) Sigma-Aldrich Cat#L3771-500G Glycerol Sigma-Aldrich Cat#56-81-5 BD Difco TM Nutrient Agar Fisher scientific Cat#DF0001-17-0 Thermo Scientific TM GeneRuler 1 kb Plus DNA Ladder, ready-to-use Thermo Scientific Cat#FERSM1334 Luria Broth Base Invitrogen Cat#12795084 GeneJET Gel Extraction Kit Thermo Scientific Cat#K0692 GeneJET Plasmid Miniprep Kit Thermo Scientific Cat#K0503 GeneJET PCR Purification Kit Thermo Scientific Cat#K0702 (Continued on next page) Cell Reports 44, 116691, December 23, 2025 15
Polymerase Chain Reaction:Article Title: Rif-seq reveals Caulobacter crescentus mRNA decay is globally coordinated with transcription and translation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Trizol Invitrogen Cat#15596018 Sucrose Sigma-Aldrich Cat#S0389-1KG Retapamulin Sigma-Aldrich Cat#SBR00057-50MG Chloramphenicol Sigma-Aldrich Cat#C0378-25G FD EcoR1 Thermo Scientific Cat#FD0274 Nhe1 Thermo Scientific Cat#FD0973 Kanamycin Gibco Cat#11815032 Xylose Sigma Aldrich Cat#X1500-500G T4 DNA ligase Thermo Scientific Cat#EL0011 Phusion DNA Polymease Thermo Scientific Cat#F530L FD Dpn1 Thermo Scientific Cat#ER1701 UltraPure TM Ethidium Bromide, 10 mg/mL Invitrogen Cat#15585011 TriTrack DNA Loading Dye (6×) Thermo Scientific Cat#R1161 Chloroform Fisher scientific Cat#AC423550010 Isopropanol Sigma-Aldrich Cat#67-63-0 Sodium Acetate (3 M), pH 5.5, RNase-free Invitrogen Cat#AM9740 GlycoBlue TM Coprecipitant Invitrogen Cat#AM9515 Ethanol Decon laboratories,inc Cat#2701 Nuclease free distilled water Invitrogen Cat#10977049 Luna® Universal One-Step RT-qPCR Kit NEB Cat#E3005L DEPC water Sigma-Aldrich Cat#693520-1L Tris (1 M), pH 8.0, RNase-free Invitrogen Cat#AM9855G MgCl2 (1 M) Invitrogen Cat#AM9530G Ammonium Chloride (99.5%) Sigma-Aldrich Cat#A9434-1KG Triton X-100 Sigma Aldrich Cat#T87T87-100ML NP-40 Surfact-Amps TM Detergent Solution Thermo Scientific Cat#85124 Magnesium sulfate Sigma-Aldrich Cat#M7506-1KG Ferrous sulfate chelate solution (100×) Sigma-Aldrich Cat#F0518-1L DNase I recombinant, RNase-free Roche Cat#4716728001 Tris (1 M), pH 7.0, RNase-free Invitrogen Cat#AM9851 Invitrogen TM Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9722 T4 PNK Thermo Scientific Cat#EK0031 Glucose (99.5%) Sigma-Aldrich Cat#G8270-1KG Bactopeptone Gibco Cat#211677 Yeast extract Milipore Cat#92144-500G-F Sodium Dodecyl Sulfate (98.5%) Sigma-Aldrich Cat#L3771-500G Glycerol Sigma-Aldrich Cat#56-81-5 BD Difco TM Nutrient Agar Fisher scientific Cat#DF0001-17-0 Thermo Scientific TM GeneRuler 1 kb Plus DNA Ladder, ready-to-use Thermo Scientific Cat#FERSM1334 Luria Broth Base Invitrogen Cat#12795084 GeneJET Gel Extraction Kit Thermo Scientific Cat#K0692 GeneJET Plasmid Miniprep Kit Thermo Scientific Cat#K0503 GeneJET PCR Purification Kit Thermo Scientific Cat#K0702 (Continued on next page) Cell Reports 44, 116691, December 23, 2025 15
Purification:Article Title: Rif-seq reveals Caulobacter crescentus mRNA decay is globally coordinated with transcription and translation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Trizol Invitrogen Cat#15596018 Sucrose Sigma-Aldrich Cat#S0389-1KG Retapamulin Sigma-Aldrich Cat#SBR00057-50MG Chloramphenicol Sigma-Aldrich Cat#C0378-25G FD EcoR1 Thermo Scientific Cat#FD0274 Nhe1 Thermo Scientific Cat#FD0973 Kanamycin Gibco Cat#11815032 Xylose Sigma Aldrich Cat#X1500-500G T4 DNA ligase Thermo Scientific Cat#EL0011 Phusion DNA Polymease Thermo Scientific Cat#F530L FD Dpn1 Thermo Scientific Cat#ER1701 UltraPure TM Ethidium Bromide, 10 mg/mL Invitrogen Cat#15585011 TriTrack DNA Loading Dye (6×) Thermo Scientific Cat#R1161 Chloroform Fisher scientific Cat#AC423550010 Isopropanol Sigma-Aldrich Cat#67-63-0 Sodium Acetate (3 M), pH 5.5, RNase-free Invitrogen Cat#AM9740 GlycoBlue TM Coprecipitant Invitrogen Cat#AM9515 Ethanol Decon laboratories,inc Cat#2701 Nuclease free distilled water Invitrogen Cat#10977049 Luna® Universal One-Step RT-qPCR Kit NEB Cat#E3005L DEPC water Sigma-Aldrich Cat#693520-1L Tris (1 M), pH 8.0, RNase-free Invitrogen Cat#AM9855G MgCl2 (1 M) Invitrogen Cat#AM9530G Ammonium Chloride (99.5%) Sigma-Aldrich Cat#A9434-1KG Triton X-100 Sigma Aldrich Cat#T87T87-100ML NP-40 Surfact-Amps TM Detergent Solution Thermo Scientific Cat#85124 Magnesium sulfate Sigma-Aldrich Cat#M7506-1KG Ferrous sulfate chelate solution (100×) Sigma-Aldrich Cat#F0518-1L DNase I recombinant, RNase-free Roche Cat#4716728001 Tris (1 M), pH 7.0, RNase-free Invitrogen Cat#AM9851 Invitrogen TM Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9722 T4 PNK Thermo Scientific Cat#EK0031 Glucose (99.5%) Sigma-Aldrich Cat#G8270-1KG Bactopeptone Gibco Cat#211677 Yeast extract Milipore Cat#92144-500G-F Sodium Dodecyl Sulfate (98.5%) Sigma-Aldrich Cat#L3771-500G Glycerol Sigma-Aldrich Cat#56-81-5 BD Difco TM Nutrient Agar Fisher scientific Cat#DF0001-17-0 Thermo Scientific TM GeneRuler 1 kb Plus DNA Ladder, ready-to-use Thermo Scientific Cat#FERSM1334 Luria Broth Base Invitrogen Cat#12795084 GeneJET Gel Extraction Kit Thermo Scientific Cat#K0692 GeneJET Plasmid Miniprep Kit Thermo Scientific Cat#K0503 GeneJET PCR Purification Kit Thermo Scientific Cat#K0702 (Continued on next page) Cell Reports 44, 116691, December 23, 2025 15
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