Computational protocol: The rnc Gene Promotes Exopolysaccharide Synthesis and Represses the vicRKX Gene Expressions via MicroRNA-Size Small RNAs in Streptococcus mutans

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Protocol publication

[…] In the S. mutans UA159 dataset, we detected 108 intergenic base pairs between the vicX and rnc genes (gb|AE014133.2|:1443948–1444056). We first analyzed these intergenic noncoding sequences by FGENESB and BPROM programs for operon and promoter prediction, respectively (http://linux1.softberry.com/berry.phtml) (Solovyev and Tatarinova, ). Co-transcription assay were conducted with templates of DNA and reverse transcribed cDNA extracted from UA159. Genomic DNA was extracted and purified by using QIAamp DNA micro Kit (QIAGEN Sciences, MD, USA) and cDNA was conducted as previously described. qPCR was performed by using the specific primes for this assay (Table ), and rnc as a reference gene. […]

Pipeline specifications

Software tools FGENESB, BPROM
Application Genome annotation
Organisms Streptococcus mutans, Rattus norvegicus
Diseases Dental Caries