Isolation:Article Title: Virulence factor discovery identifies associations between the Fic gene family and Fap2 + fusobacteria in colorectal cancer microbiomes.
Article Snippet: .. Total RNA was then isolated using QIAzol Lysis Reagent in combination with Max Bacterial Enhancement Reagent (Thermo Fisher Scientific, Waltham, MA) and purified using the Direct-zol RNA Miniprep Kit with on-column DNA digestion (Zymo Research, Irvine, CA) followed by double DNAse treatment with TURBO DNA-free Kit (Thermo Fisher Scientific, Waltham, MA). .. Complementary DNA (cDNA) was synthesized from 5 μg RNA using Maxima H Minus cDNA Synthesis Master Mix (Thermo Fisher Scientific, Waltham, MA) and subjected to RT-qPCR analysis (40 ng per technical duplicate) using the KAPA SYBR FAST Universal Kit (Roche) on an Agilent Mx3005P cycler.
Article Title: Virulence factor discovery identifies associations between the Fic gene family and Fap2 + fusobacteria in colorectal cancer microbiomes
Article Snippet: .. Total RNA was then isolated using QIAzol Lysis Reagent in combination with Max Bacterial Enhancement Reagent (Thermo Fisher Scientific, Waltham, MA) and purified using the Direct-zol RNA Miniprep Kit with on-column DNA digestion (Zymo Research, Irvine, CA) followed by double DNAse treatment with TURBO DNA-free Kit (Thermo Fisher Scientific, Waltham, MA). .. Complementary DNA (cDNA) was synthesized from 5 μg RNA using Maxima H Minus cDNA Synthesis Master Mix (Thermo Fisher Scientific, Waltham, MA) and subjected to RT-qPCR analysis (40 ng per technical duplicate) using the KAPA SYBR FAST Universal Kit (Roche) on an Agilent Mx3005P cycler.
Article Title: Exaiptasia pallida Infection Model Reveals the Critical Role of Vibrio parahaemolyticus T3SS Virulence Factors in Its Pathogenicity for Sea Anemones
Article Snippet: .. The pellet was resuspended into 200 μL of Max Bacterial Enhancement Reagent (TRIzol Max Bacterial RNA Isolation Kit from Thermo Fisher Scientific, Waltham, MA, USA) and incubated at 95 ◦C for 4 min. A volume of 1 mL of TRIzol was then added to the reaction, and after an incubation of 5 min at room temperature, 200 μL of cold chloroform was added, and the reaction was hand-shaken for 15 s and let to settle at room temperature for 5 min. After centrifugation at 12,000× g for 15 min at 4 ◦C, the aqueous phase was then transferred to an equal volume of chilled 100% ethanol and moved onto a column for purification. .. The purification, including a DNase treatment step, followed the Directzol RNA MiniPrep Plus protocol (cat# R207 from Zymoresearch, Irvine, CA, USA).
Article Title: Exaiptasia pallida Infection Model Reveals the Critical Role of Vibrio parahaemolyticus T3SS Virulence Factors in Its Pathogenicity for Sea Anemones
Article Snippet: .. The pellet was resuspended into 200 μL of Max Bacterial Enhancement Reagent (TRIzol Max Bacterial RNA Isolation Kit from Thermo Fisher Scientific, Waltham, MA, USA) and incubated at 95 °C for 4 min. A volume of 1 mL of TRIzol was then added to the reaction, and after an incubation of 5 min at room temperature, 200 μL of cold chloroform was added, and the reaction was hand-shaken for 15 s and let to settle at room temperature for 5 min. After centrifugation at 12,000× g for 15 min at 4 °C, the aqueous phase was then transferred to an equal volume of chilled 100% ethanol and moved onto a column for purification. .. The purification, including a DNase treatment step, followed the Directzol RNA MiniPrep Plus protocol (cat# R207 from Zymoresearch, Irvine, CA, USA).
Lysis:Article Title: Virulence factor discovery identifies associations between the Fic gene family and Fap2 + fusobacteria in colorectal cancer microbiomes.
Article Snippet: .. Total RNA was then isolated using QIAzol Lysis Reagent in combination with Max Bacterial Enhancement Reagent (Thermo Fisher Scientific, Waltham, MA) and purified using the Direct-zol RNA Miniprep Kit with on-column DNA digestion (Zymo Research, Irvine, CA) followed by double DNAse treatment with TURBO DNA-free Kit (Thermo Fisher Scientific, Waltham, MA). .. Complementary DNA (cDNA) was synthesized from 5 μg RNA using Maxima H Minus cDNA Synthesis Master Mix (Thermo Fisher Scientific, Waltham, MA) and subjected to RT-qPCR analysis (40 ng per technical duplicate) using the KAPA SYBR FAST Universal Kit (Roche) on an Agilent Mx3005P cycler.
Article Title: Virulence factor discovery identifies associations between the Fic gene family and Fap2 + fusobacteria in colorectal cancer microbiomes
Article Snippet: .. Total RNA was then isolated using QIAzol Lysis Reagent in combination with Max Bacterial Enhancement Reagent (Thermo Fisher Scientific, Waltham, MA) and purified using the Direct-zol RNA Miniprep Kit with on-column DNA digestion (Zymo Research, Irvine, CA) followed by double DNAse treatment with TURBO DNA-free Kit (Thermo Fisher Scientific, Waltham, MA). .. Complementary DNA (cDNA) was synthesized from 5 μg RNA using Maxima H Minus cDNA Synthesis Master Mix (Thermo Fisher Scientific, Waltham, MA) and subjected to RT-qPCR analysis (40 ng per technical duplicate) using the KAPA SYBR FAST Universal Kit (Roche) on an Agilent Mx3005P cycler.
Article Title: tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector
Article Snippet: .. Cell lysis was done using Max Bacterial Enhancement Reagent (Invitrogen) for 4 min and then with TRIzol reagent (Invitrogen) for 5 min. Total RNA including small RNAs (>17 nt) was purified using a Zymo-Spin column (Direct-zol RNA kit, Zymo Research). .. RNA was treated with Turbo DNase (Turbo DNA-free kit, Invitrogen) to remove DNA contamination.
Purification:Article Title: Virulence factor discovery identifies associations between the Fic gene family and Fap2 + fusobacteria in colorectal cancer microbiomes.
Article Snippet: .. Total RNA was then isolated using QIAzol Lysis Reagent in combination with Max Bacterial Enhancement Reagent (Thermo Fisher Scientific, Waltham, MA) and purified using the Direct-zol RNA Miniprep Kit with on-column DNA digestion (Zymo Research, Irvine, CA) followed by double DNAse treatment with TURBO DNA-free Kit (Thermo Fisher Scientific, Waltham, MA). .. Complementary DNA (cDNA) was synthesized from 5 μg RNA using Maxima H Minus cDNA Synthesis Master Mix (Thermo Fisher Scientific, Waltham, MA) and subjected to RT-qPCR analysis (40 ng per technical duplicate) using the KAPA SYBR FAST Universal Kit (Roche) on an Agilent Mx3005P cycler.
Article Title: Virulence factor discovery identifies associations between the Fic gene family and Fap2 + fusobacteria in colorectal cancer microbiomes
Article Snippet: .. Total RNA was then isolated using QIAzol Lysis Reagent in combination with Max Bacterial Enhancement Reagent (Thermo Fisher Scientific, Waltham, MA) and purified using the Direct-zol RNA Miniprep Kit with on-column DNA digestion (Zymo Research, Irvine, CA) followed by double DNAse treatment with TURBO DNA-free Kit (Thermo Fisher Scientific, Waltham, MA). .. Complementary DNA (cDNA) was synthesized from 5 μg RNA using Maxima H Minus cDNA Synthesis Master Mix (Thermo Fisher Scientific, Waltham, MA) and subjected to RT-qPCR analysis (40 ng per technical duplicate) using the KAPA SYBR FAST Universal Kit (Roche) on an Agilent Mx3005P cycler.
Article Title: tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector
Article Snippet: .. Cell lysis was done using Max Bacterial Enhancement Reagent (Invitrogen) for 4 min and then with TRIzol reagent (Invitrogen) for 5 min. Total RNA including small RNAs (>17 nt) was purified using a Zymo-Spin column (Direct-zol RNA kit, Zymo Research). .. RNA was treated with Turbo DNase (Turbo DNA-free kit, Invitrogen) to remove DNA contamination.
Article Title: Exaiptasia pallida Infection Model Reveals the Critical Role of Vibrio parahaemolyticus T3SS Virulence Factors in Its Pathogenicity for Sea Anemones
Article Snippet: .. The pellet was resuspended into 200 μL of Max Bacterial Enhancement Reagent (TRIzol Max Bacterial RNA Isolation Kit from Thermo Fisher Scientific, Waltham, MA, USA) and incubated at 95 ◦C for 4 min. A volume of 1 mL of TRIzol was then added to the reaction, and after an incubation of 5 min at room temperature, 200 μL of cold chloroform was added, and the reaction was hand-shaken for 15 s and let to settle at room temperature for 5 min. After centrifugation at 12,000× g for 15 min at 4 ◦C, the aqueous phase was then transferred to an equal volume of chilled 100% ethanol and moved onto a column for purification. .. The purification, including a DNase treatment step, followed the Directzol RNA MiniPrep Plus protocol (cat# R207 from Zymoresearch, Irvine, CA, USA).
Article Title: Exaiptasia pallida Infection Model Reveals the Critical Role of Vibrio parahaemolyticus T3SS Virulence Factors in Its Pathogenicity for Sea Anemones
Article Snippet: .. The pellet was resuspended into 200 μL of Max Bacterial Enhancement Reagent (TRIzol Max Bacterial RNA Isolation Kit from Thermo Fisher Scientific, Waltham, MA, USA) and incubated at 95 °C for 4 min. A volume of 1 mL of TRIzol was then added to the reaction, and after an incubation of 5 min at room temperature, 200 μL of cold chloroform was added, and the reaction was hand-shaken for 15 s and let to settle at room temperature for 5 min. After centrifugation at 12,000× g for 15 min at 4 °C, the aqueous phase was then transferred to an equal volume of chilled 100% ethanol and moved onto a column for purification. .. The purification, including a DNase treatment step, followed the Directzol RNA MiniPrep Plus protocol (cat# R207 from Zymoresearch, Irvine, CA, USA).
other:Article Title: The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli
Article Snippet: The supernatant was removed and the pellet was resuspended in 200 μL of Max Bacterial Enhancement Reagent (TRIzol® MaxTM Bacterial RNA Isolation Kit, Ambion®, life TechnologiesTM) pre-heated to 95 °C.
RNA Extraction:Article Title: High-throughput, Multiplexed Assay Platform for Integrated Analysis of Sepsis
Article Snippet: Bacteria were seeded and cultured in suspension using the following media: S. aureus (#25923) in Staphylococcus broth (BD Biosciences); Enterococcus faecalis (#29212) in trypticase soy broth containing 5% defibrinated sheep blood (Hemostat Laboratories); E. coli (#25922) in Luria-Bertani (LB) media (BD Biosciences); Pseudomonas aeruginosa (#142), Klebsiella pneumoniae (#43816) in trypticase soy broth. .. For RNA extraction, bacteria were first centrifuged (6,000 × g, 10 min), and pellets were treated with Max Bacterial Enhancement Reagent (Life Technologies), then lysed using TRIzol (Life Technologies). .. After solvent extraction of the RNA followed by precipitation and washing, the final RNA yield was measured using Nanodrop OneC spectrophotometer (Thermofisher).
Bacteria:Article Title: High-throughput, Multiplexed Assay Platform for Integrated Analysis of Sepsis
Article Snippet: Bacteria were seeded and cultured in suspension using the following media: S. aureus (#25923) in Staphylococcus broth (BD Biosciences); Enterococcus faecalis (#29212) in trypticase soy broth containing 5% defibrinated sheep blood (Hemostat Laboratories); E. coli (#25922) in Luria-Bertani (LB) media (BD Biosciences); Pseudomonas aeruginosa (#142), Klebsiella pneumoniae (#43816) in trypticase soy broth. .. For RNA extraction, bacteria were first centrifuged (6,000 × g, 10 min), and pellets were treated with Max Bacterial Enhancement Reagent (Life Technologies), then lysed using TRIzol (Life Technologies). .. After solvent extraction of the RNA followed by precipitation and washing, the final RNA yield was measured using Nanodrop OneC spectrophotometer (Thermofisher).
Incubation:Article Title: Exaiptasia pallida Infection Model Reveals the Critical Role of Vibrio parahaemolyticus T3SS Virulence Factors in Its Pathogenicity for Sea Anemones
Article Snippet: .. The pellet was resuspended into 200 μL of Max Bacterial Enhancement Reagent (TRIzol Max Bacterial RNA Isolation Kit from Thermo Fisher Scientific, Waltham, MA, USA) and incubated at 95 ◦C for 4 min. A volume of 1 mL of TRIzol was then added to the reaction, and after an incubation of 5 min at room temperature, 200 μL of cold chloroform was added, and the reaction was hand-shaken for 15 s and let to settle at room temperature for 5 min. After centrifugation at 12,000× g for 15 min at 4 ◦C, the aqueous phase was then transferred to an equal volume of chilled 100% ethanol and moved onto a column for purification. .. The purification, including a DNase treatment step, followed the Directzol RNA MiniPrep Plus protocol (cat# R207 from Zymoresearch, Irvine, CA, USA).
Article Title: Exaiptasia pallida Infection Model Reveals the Critical Role of Vibrio parahaemolyticus T3SS Virulence Factors in Its Pathogenicity for Sea Anemones
Article Snippet: .. The pellet was resuspended into 200 μL of Max Bacterial Enhancement Reagent (TRIzol Max Bacterial RNA Isolation Kit from Thermo Fisher Scientific, Waltham, MA, USA) and incubated at 95 °C for 4 min. A volume of 1 mL of TRIzol was then added to the reaction, and after an incubation of 5 min at room temperature, 200 μL of cold chloroform was added, and the reaction was hand-shaken for 15 s and let to settle at room temperature for 5 min. After centrifugation at 12,000× g for 15 min at 4 °C, the aqueous phase was then transferred to an equal volume of chilled 100% ethanol and moved onto a column for purification. .. The purification, including a DNase treatment step, followed the Directzol RNA MiniPrep Plus protocol (cat# R207 from Zymoresearch, Irvine, CA, USA).
Centrifugation:Article Title: Exaiptasia pallida Infection Model Reveals the Critical Role of Vibrio parahaemolyticus T3SS Virulence Factors in Its Pathogenicity for Sea Anemones
Article Snippet: .. The pellet was resuspended into 200 μL of Max Bacterial Enhancement Reagent (TRIzol Max Bacterial RNA Isolation Kit from Thermo Fisher Scientific, Waltham, MA, USA) and incubated at 95 ◦C for 4 min. A volume of 1 mL of TRIzol was then added to the reaction, and after an incubation of 5 min at room temperature, 200 μL of cold chloroform was added, and the reaction was hand-shaken for 15 s and let to settle at room temperature for 5 min. After centrifugation at 12,000× g for 15 min at 4 ◦C, the aqueous phase was then transferred to an equal volume of chilled 100% ethanol and moved onto a column for purification. .. The purification, including a DNase treatment step, followed the Directzol RNA MiniPrep Plus protocol (cat# R207 from Zymoresearch, Irvine, CA, USA).
Article Title: Exaiptasia pallida Infection Model Reveals the Critical Role of Vibrio parahaemolyticus T3SS Virulence Factors in Its Pathogenicity for Sea Anemones
Article Snippet: .. The pellet was resuspended into 200 μL of Max Bacterial Enhancement Reagent (TRIzol Max Bacterial RNA Isolation Kit from Thermo Fisher Scientific, Waltham, MA, USA) and incubated at 95 °C for 4 min. A volume of 1 mL of TRIzol was then added to the reaction, and after an incubation of 5 min at room temperature, 200 μL of cold chloroform was added, and the reaction was hand-shaken for 15 s and let to settle at room temperature for 5 min. After centrifugation at 12,000× g for 15 min at 4 °C, the aqueous phase was then transferred to an equal volume of chilled 100% ethanol and moved onto a column for purification. .. The purification, including a DNase treatment step, followed the Directzol RNA MiniPrep Plus protocol (cat# R207 from Zymoresearch, Irvine, CA, USA).
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