Bacterial Gene Selection for Analysis

The pool of candidate reference targets comprised 11 bacterial genes. Nine of them (16S rRNA, 23S rRNA, dnaK, groEL, gyrB, recA, rho, rpoB, rpoD) were chosen based on literature data. Homologues of these sequences were derived from the complete genome of O. quorumnocens A44 (CP022602.1–CP022605.1) (detailed list of loci in Table 2). The two other genes were: gfp, carried on the artificially introduced vector pPROBE-GTkan^{45 (link)} and CES85_4722, a hypothetical A44 gene with no data concerning its stability (a blind control). All PCR primers (Supplementary Table S1) were designed using the Primer3Plus software^{78 (link),79 (link)} (http://primer3plus.com/). Specificity of the primers was verified using real-time PCR followed by melt curve analysis and electrophoresis in 1.2% agarose gel (TopVision, Thermo Scientific).

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Krzyżanowska D.M., Supernat A., Maciąg T., Matuszewska M, & Jafra S. (2019). Selection of reference genes for measuring the expression of aiiO in Ochrobactrum quorumnocens A44 using RT-qPCR. Scientific Reports, 9, 13129.

Publication 2019

TopVision

16s rrna 23s rrna A gene Bacterial genes Blind Electrophoresis agarose gel Genes Genome Primers Real time pcr Sequences homologues Vector

Corresponding Organization :

Other organizations : Gdańsk Medical University

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Variable analysis

independent variables

Homologues of 9 bacterial genes (16S rRNA, 23S rRNA, dnaK, groEL, gyrB, recA, rho, rpoB, rpoD) from the complete genome of O. quorumnocens A44
Gfp gene carried on the artificially introduced vector pPROBE-GTkan
CES85_4722, a hypothetical A44 gene with no data concerning its stability

dependent variables

No dependent variables are explicitly mentioned in the given information.

control variables

The pool of candidate reference targets comprised 11 bacterial genes.
PCR primers were designed using the Primer3Plus software, and their specificity was verified using real-time PCR followed by melt curve analysis and electrophoresis in 1.2% agarose gel.

controls

Positive control: 9 bacterial genes (16S rRNA, 23S rRNA, dnaK, groEL, gyrB, recA, rho, rpoB, rpoD) chosen based on literature data.
Negative control: CES85_4722, a hypothetical A44 gene with no data concerning its stability (a blind control).

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