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Additionally, we performed RNA-seq on a pool of epidermal melanocytes to determine a reference level of expression for each gene in normal melanocytic cells (see Materials and Methods).
For each sample, a no-reverse transcription control was used, and HPRT was used as reference level of expression.
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The dashed red line represents the iBAQ value of genes that are not targeted by any miRNAs identified in this study and serves as a background, reference level of protein expression.
To quantify tissue specificity, we applied a binary score to expression in each tissue without reference to level of expression.
The appropriate application of quantitative real-time PCR (RT-qPCR), however, requires the use of reference genes whose level of expression is not affected by the test, by general physiological conditions or by inter-individual variability.
Although the community-accumulated tool set for the molecular analysis of Neurospora is extensive, two components are missing: (1) dependable reference genes whose level of expression are relatively constant across light/dark cycles and as a function of time of day and (2) a catalog of primers specifically designed for real-time PCR (RT-PCR).
A subset of more highly expressed rye reference sequences with a minimum level of expression of at least 10 transcripts in any rye tissue-specific library and not detected in all triticale libraries were selected for further analysis.
However, there were concerns for the use of 18S gene as a reference, as its much greater level of expression relative to target mRNA (Tang et al. 2007).
The modified siRNAs caused significant gene silencing as observed for the non-modified reference duplex, with the highest remaining level of expression of about 10% observed for "SIR Az-G14 as".
Conceptually, an ideal gene selected as an internal reference control should have a constant level of expression across the tissue or cell samples used throughout the experiment, and should not exhibit altered expression with diseased or, control tissues, or indeed experimental conditions [ 10].
Porcine miRNAs frequently exhibit variation from their "reference" miRBase sequences (which have the highest level of expression), producing multiple mature variants that we herein refer to as isomiRs [ 22- 24].
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