Determination of stable housekeeping genes
, differentially regulated target genes and sample integrity: BestKeeper-Excel-based tool using pair-wise correlations.
For example, for strains from dyads 10 and 12, the ompA was D2, but the sequences of the 7 housekeeping genes
(MLST ST34) matched the 7 housekeeping genes
of strain F/ICCal3 from the MLST database.
To address whether the QIAzol method selectively affects transcripts with different abundances, we also evaluated gene expression with the ACTB gene, which is commonly monitored as a housekeeping gene
In this study, the reaction of housekeeping genes
The 18S was used as a housekeeping gene
to normalize the data.
To avoid variations because of different sample amounts, standardization with housekeeping genes
was the method of choice.
Transposable elements, the promoter regions of housekeeping genes
, and cis-acting regulatory elements of imprinted genes are three key epigenetic susceptibility targets containing CpG sites that are normally methylated, unmethylated, and differentially methylated, respectively.
Each well includes one user-defined target, three housekeeping genes
and one procedural control to ensure assay quality.
pseudomallei is multilocus sequence typing (MLST), which is based on a comparison of the alleles of 7 housekeeping genes
to generate a sequence type (ST) (2).
Usually, the well-known housekeeping genes
are chosen such as the glyceraldehydes-3-phosphate dehydrogenase (GAPDH), [alpha]-actins (ACTB), hypoxantine phosphoribosyltransferase (HRPT), [beta]-tubulin (TUB), elongation factor 1 alpha (EF1A) and 18S, 28S rRNA (Shu et al.
The primers used to amplify the target (actin and elongation factor [EF] 2) and housekeeping genes
(EF-1, S-18, and ubiquitin), and their respective efficiencies are listed in Table 1.
In Chapter 3, the authors cover topics such as the quality and quantity of the labeled target, the use of housekeeping genes
and other controls, imaging of the arrays, and initial statistical and data analysis steps.