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Early success was limited by the lack of suitable primers.
The probes were selected from a range of strength of association signals based on the availability of suitable primers.
This might be due to the lack of suitable primers for the amplification of variable regions of the mitochondrial genome.
Based on the extent of the differential methylation grade, the importance of the biological functions, the design of suitable primers and the availability of antibodies, we decided to validate DIO3 and FOXD2 by methylation-specific PCR (MSP) and pyrosequencing, respectively, and by quantitative polymerase chain reaction (qPCR) and immunohistochemistry (IHC) for both.
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The choice of suitable primer sets is thereby critical to obtain optimal qPCR results.
Third, inclusion of degenerate bases might have led to amplification failure due to the reduced concentration of suitable primer.
Unfortunately, due to the lack of suitable primer combinations, the very 5'-end of the actin I sequence could not be analysed.
Effective and efficient genotyping of any plant species through RAPD requires a careful selection of suitable primer combination in order to get detail and informative result.
The genes were selected from the list of rapidly evolving sex-associated genes based on their high dN/dS and the existence of suitable primer sites in the 4-way alignment.
The five candidate genes were chosen from the list of rapidly evolving sex-associated genes (Table 3) based on their higher than mean dN/dS and existence of suitable primer sites in the 4-way alignment.
Of note, Os04g0582600 was not considered here because of difficulties in generating suitable primers for qRT-PCR.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com