Acrylamide Gel Assay:Article Title: Virus replication in the honey bee parasite, Varroa destructor .
Article Snippet: Small RNA libraries were purified with the Monarch PCR Cleanup Kit (NEB) prior to size selection to obtain the correct fragment sizes for small RNA analysis. .. Libraries were mixed with Novex 5× Hi-Density TBE Sample Loading Dye (Thermo Fisher), then loaded into a 6% TBE acrylamide gel with the Quick-Load pBR322 DNA-MspI Digest ladder, and run for 65 minutes at 120 V. Gels were stained with SYBR Gold (Thermo Fisher) in 6% TBE buffer for 3 minutes, prior to size selection under a UV transilluminator. .. The region encompassing the small RNA size range of interest (15–35 nt, corresponding to the size ladder bands at 147–160 nt) was excised and purified by first passing through gel breaker tubes in DNA Gel elution buffer (NEB), incubated overnight at 4°C with shaking, then precipitated with 100% EtOH, 3 M sodium acetate (pH 5.5), and 2 μL glycogen for 4 hours at −80°C.
Article Title: Virus replication in the honey bee parasite, Varroa destructor
Article Snippet: Small RNA libraries were purified with the Monarch PCR Cleanup Kit (NEB) prior to size selection to obtain the correct fragment sizes for small RNA analysis. .. Libraries were mixed with Novex 5× Hi-Density TBE Sample Loading Dye (Thermo Fisher), then loaded into a 6% TBE acrylamide gel with the Quick-Load pBR322 DNA-MspI Digest ladder, and run for 65 minutes at 120 V. Gels were stained with SYBR Gold (Thermo Fisher) in 6% TBE buffer for 3 minutes, prior to size selection under a UV transilluminator. .. The region encompassing the small RNA size range of interest (15–35 nt, corresponding to the size ladder bands at 147–160 nt) was excised and purified by first passing through gel breaker tubes in DNA Gel elution buffer (NEB), incubated overnight at 4°C with shaking, then precipitated with 100% EtOH, 3 M sodium acetate (pH 5.5), and 2 μL glycogen for 4 hours at −80°C.
Article Title: Temperature-dependent modulation of aberrant influenza A virus RNA synthesis affects innate immune signaling
Article Snippet: .. The PCR products were resolved on a 10% TBE acrylamide gel and visualized using SYBR Gold (Invitrogen). ..
Article Title: A HigB-like toxin promotes non-replicating Salmonella inside macrophages by inhibiting ribonuclease III
Article Snippet: .. The reaction products were analyzed by 15% denaturing TBE acrylamide gel containing 7 M urea and electrophoresed at 15 W for 25 min. Gels were stained using SYBR Gold (ThermoFisher, S11494) and visualized by UV detector (EMBI TEC, PI-1000). .. To detect rRNA cleavage by SehA toxin in vivo , Salmonella strains harboring either the SehA-expressing plasmid or the empty vector were grown in N-minimal media containing 0.01 mM Mg 2+ .
Article Title: Virus replication in the honey bee parasite, Varroa destructor
Article Snippet: Small RNA libraries were purified with the Monarch PCR Cleanup Kit (NEB) prior to size selection to obtain the correct fragment sizes for small RNA analysis. .. Libraries were mixed with Novex 5X Hi-Density TBE Sample Loading Dye (Thermofisher), then loaded into a 6% TBE acrylamide gel with the Quick-Load pBR322 DNA-MspI Digest ladder and run for 65 minutes at 120 V. Gels were stained with SYBR Gold (Thermofisher) in 6% TBE buffer for 3 minutes, prior to size selection under a UV transilluminator. .. The region encompassing the small RNA size range of interest (15-35 nt, corresponding to the size ladder bands at 147 - 160 nt) was excised and purified by first passing through gel breaker tubes in DNA Gel elution buffer (NEB), incubated overnight at 4° C with shaking, then precipitated with 100% EtOH, 3M sodium acetate (pH 5.5) and 2 μl glycogen for 4 hours at -80° C. The pellets were resuspended in 11 μl of TE buffer, and the sRNA libraries were shipped to the Australian Genome Research Facility (AGRF) for sequencing with Illumina HiSeq or Illumina NovaSeq 6000 (100bp SE).
Article Title: DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors
Article Snippet: .. Gel electrophoresis was executed with a 12-well 10% TBE acrylamide gel from Invitrogen in 1X TBE buffer prepared in-house. ..
Staining:Article Title: Virus replication in the honey bee parasite, Varroa destructor .
Article Snippet: Small RNA libraries were purified with the Monarch PCR Cleanup Kit (NEB) prior to size selection to obtain the correct fragment sizes for small RNA analysis. .. Libraries were mixed with Novex 5× Hi-Density TBE Sample Loading Dye (Thermo Fisher), then loaded into a 6% TBE acrylamide gel with the Quick-Load pBR322 DNA-MspI Digest ladder, and run for 65 minutes at 120 V. Gels were stained with SYBR Gold (Thermo Fisher) in 6% TBE buffer for 3 minutes, prior to size selection under a UV transilluminator. .. The region encompassing the small RNA size range of interest (15–35 nt, corresponding to the size ladder bands at 147–160 nt) was excised and purified by first passing through gel breaker tubes in DNA Gel elution buffer (NEB), incubated overnight at 4°C with shaking, then precipitated with 100% EtOH, 3 M sodium acetate (pH 5.5), and 2 μL glycogen for 4 hours at −80°C.
Article Title: Virus replication in the honey bee parasite, Varroa destructor
Article Snippet: Small RNA libraries were purified with the Monarch PCR Cleanup Kit (NEB) prior to size selection to obtain the correct fragment sizes for small RNA analysis. .. Libraries were mixed with Novex 5× Hi-Density TBE Sample Loading Dye (Thermo Fisher), then loaded into a 6% TBE acrylamide gel with the Quick-Load pBR322 DNA-MspI Digest ladder, and run for 65 minutes at 120 V. Gels were stained with SYBR Gold (Thermo Fisher) in 6% TBE buffer for 3 minutes, prior to size selection under a UV transilluminator. .. The region encompassing the small RNA size range of interest (15–35 nt, corresponding to the size ladder bands at 147–160 nt) was excised and purified by first passing through gel breaker tubes in DNA Gel elution buffer (NEB), incubated overnight at 4°C with shaking, then precipitated with 100% EtOH, 3 M sodium acetate (pH 5.5), and 2 μL glycogen for 4 hours at −80°C.
Article Title: A HigB-like toxin promotes non-replicating Salmonella inside macrophages by inhibiting ribonuclease III
Article Snippet: .. The reaction products were analyzed by 15% denaturing TBE acrylamide gel containing 7 M urea and electrophoresed at 15 W for 25 min. Gels were stained using SYBR Gold (ThermoFisher, S11494) and visualized by UV detector (EMBI TEC, PI-1000). .. To detect rRNA cleavage by SehA toxin in vivo , Salmonella strains harboring either the SehA-expressing plasmid or the empty vector were grown in N-minimal media containing 0.01 mM Mg 2+ .
Article Title: Virus replication in the honey bee parasite, Varroa destructor
Article Snippet: Small RNA libraries were purified with the Monarch PCR Cleanup Kit (NEB) prior to size selection to obtain the correct fragment sizes for small RNA analysis. .. Libraries were mixed with Novex 5X Hi-Density TBE Sample Loading Dye (Thermofisher), then loaded into a 6% TBE acrylamide gel with the Quick-Load pBR322 DNA-MspI Digest ladder and run for 65 minutes at 120 V. Gels were stained with SYBR Gold (Thermofisher) in 6% TBE buffer for 3 minutes, prior to size selection under a UV transilluminator. .. The region encompassing the small RNA size range of interest (15-35 nt, corresponding to the size ladder bands at 147 - 160 nt) was excised and purified by first passing through gel breaker tubes in DNA Gel elution buffer (NEB), incubated overnight at 4° C with shaking, then precipitated with 100% EtOH, 3M sodium acetate (pH 5.5) and 2 μl glycogen for 4 hours at -80° C. The pellets were resuspended in 11 μl of TE buffer, and the sRNA libraries were shipped to the Australian Genome Research Facility (AGRF) for sequencing with Illumina HiSeq or Illumina NovaSeq 6000 (100bp SE).
Size Selection:Article Title: Virus replication in the honey bee parasite, Varroa destructor .
Article Snippet: Small RNA libraries were purified with the Monarch PCR Cleanup Kit (NEB) prior to size selection to obtain the correct fragment sizes for small RNA analysis. .. Libraries were mixed with Novex 5× Hi-Density TBE Sample Loading Dye (Thermo Fisher), then loaded into a 6% TBE acrylamide gel with the Quick-Load pBR322 DNA-MspI Digest ladder, and run for 65 minutes at 120 V. Gels were stained with SYBR Gold (Thermo Fisher) in 6% TBE buffer for 3 minutes, prior to size selection under a UV transilluminator. .. The region encompassing the small RNA size range of interest (15–35 nt, corresponding to the size ladder bands at 147–160 nt) was excised and purified by first passing through gel breaker tubes in DNA Gel elution buffer (NEB), incubated overnight at 4°C with shaking, then precipitated with 100% EtOH, 3 M sodium acetate (pH 5.5), and 2 μL glycogen for 4 hours at −80°C.
Article Title: Virus replication in the honey bee parasite, Varroa destructor
Article Snippet: Small RNA libraries were purified with the Monarch PCR Cleanup Kit (NEB) prior to size selection to obtain the correct fragment sizes for small RNA analysis. .. Libraries were mixed with Novex 5× Hi-Density TBE Sample Loading Dye (Thermo Fisher), then loaded into a 6% TBE acrylamide gel with the Quick-Load pBR322 DNA-MspI Digest ladder, and run for 65 minutes at 120 V. Gels were stained with SYBR Gold (Thermo Fisher) in 6% TBE buffer for 3 minutes, prior to size selection under a UV transilluminator. .. The region encompassing the small RNA size range of interest (15–35 nt, corresponding to the size ladder bands at 147–160 nt) was excised and purified by first passing through gel breaker tubes in DNA Gel elution buffer (NEB), incubated overnight at 4°C with shaking, then precipitated with 100% EtOH, 3 M sodium acetate (pH 5.5), and 2 μL glycogen for 4 hours at −80°C.
Article Title: Virus replication in the honey bee parasite, Varroa destructor
Article Snippet: Small RNA libraries were purified with the Monarch PCR Cleanup Kit (NEB) prior to size selection to obtain the correct fragment sizes for small RNA analysis. .. Libraries were mixed with Novex 5X Hi-Density TBE Sample Loading Dye (Thermofisher), then loaded into a 6% TBE acrylamide gel with the Quick-Load pBR322 DNA-MspI Digest ladder and run for 65 minutes at 120 V. Gels were stained with SYBR Gold (Thermofisher) in 6% TBE buffer for 3 minutes, prior to size selection under a UV transilluminator. .. The region encompassing the small RNA size range of interest (15-35 nt, corresponding to the size ladder bands at 147 - 160 nt) was excised and purified by first passing through gel breaker tubes in DNA Gel elution buffer (NEB), incubated overnight at 4° C with shaking, then precipitated with 100% EtOH, 3M sodium acetate (pH 5.5) and 2 μl glycogen for 4 hours at -80° C. The pellets were resuspended in 11 μl of TE buffer, and the sRNA libraries were shipped to the Australian Genome Research Facility (AGRF) for sequencing with Illumina HiSeq or Illumina NovaSeq 6000 (100bp SE).
Polymerase Chain Reaction:Article Title: Temperature-dependent modulation of aberrant influenza A virus RNA synthesis affects innate immune signaling
Article Snippet: .. The PCR products were resolved on a 10% TBE acrylamide gel and visualized using SYBR Gold (Invitrogen). ..
Nucleic Acid Electrophoresis:Article Title: DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors
Article Snippet: .. Gel electrophoresis was executed with a 12-well 10% TBE acrylamide gel from Invitrogen in 1X TBE buffer prepared in-house. ..
Article Title: DNA-encoded chemistry technology yields expedient access to SARS-CoV-2 M pro inhibitors
Article Snippet: .. Gel electrophoresis was executed with a 12-well 10% TBE acrylamide gel from Invitrogen in 1X TBE buffer prepared in-house. ..
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