Specific primer pairs were designed at appropriate positions of the putative viral contigs using the CLC Genomics Workbench 11 and the Primer Premier 5.0 (Premier Biosoft, Palo Alto, CA, USA) to amplify overlapping fragments (Supplementary Table S4 ). Then, a one-step reverse transcription-PCR (RT-PCR) assay was conducted with a PrimeScript kit (Takara, Tokyo, Japan), and viral genomic terminal sequences were determined using commercial 5′ and 3′ RACE (rapid amplification of cDNA ends) kits (Invitrogen, Waltham, MA, USA). The PCR products were gel-purified using the Gel Extraction Kit (OMEGA Bio-Tec Inc., Doraville, GA, USA) and cloned on pEASY-T1 vectors (TransGen, Beijing, China) using competent cells. Five clones of each amplicon were fully sequenced with primer in both directions (Tsingke, Chengdu, China), and the output sequences were de novo assembled in the SeqMan program (DNAStar, Madison, WI, USA).
Clc genomics workbench 11
Manufactured by Premier Biosoft
Sourced in United States
CLC Genomics Workbench 11 is a comprehensive software suite designed for advanced genomic data analysis. It provides a user-friendly interface and a wide range of tools for tasks such as sequence assembly, annotation, and comparative analysis.
Automatically generated - may contain errors
2 protocols using clc genomics workbench 11
1
Complete Viral Genome Sequencing
2
Viral Genome Sequencing and Assembly
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Specific primer pairs were designed at appropriate positions of the viral contigs to amplify overlapping fragments using the CLC Genomics Workbench 11 and the Primer Premier 5.0 (Premier Biosoft, Palo Alto, CA, USA). Thereafter, a one-step reverse transcription-PCR (RT-PCR) assay was conducted with a PrimeScript kit (Takara, Tokyo, Japan), and Viral genomic terminal sequences were determined using commercial 5′ and 3′ RACE (rapid amplification of cDNA ends) kits (Invitrogen, Waltham, MA, USA).
The PCR products were gel-purified using the Gel Extraction Kit (OMEGA Bio-Tec Inc., Doraville, GA, USA) and cloned on pEASY-T1 Vectors (TransGen, Beijing, China) using competent cells. Five clones of each amplicon were fully sequenced with primer in both directions (Tsingke, Chengdu, China), and the output sequences were de novo assembled in the SeqMan program (DNAStar, Madison, WI, USA).
The PCR products were gel-purified using the Gel Extraction Kit (OMEGA Bio-Tec Inc., Doraville, GA, USA) and cloned on pEASY-T1 Vectors (TransGen, Beijing, China) using competent cells. Five clones of each amplicon were fully sequenced with primer in both directions (Tsingke, Chengdu, China), and the output sequences were de novo assembled in the SeqMan program (DNAStar, Madison, WI, USA).
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