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The levels of β-actin transcripts were measured by RT-PCR in normalized samples of transfected or non-transfected cells.
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High Id4 expression was observed in normal samples (normalized to 1 in ΔΔCt calculation) showing no Id4 promoter methylation.
The sample was also known to have DNA amplification of EGFR, "epidermal growth factor receptor", and a focused observation indicated ~25× fold more reads mapping to the EGFR exons in tumor sample than in normal sample (normalized to average coverage of all targeted exons across the whole genome) when single hybridization capture protocol was applied to both samples.
The reduction in the abundance of the frequent clone, used as a radioactive probe, in the normalized sample became evident since much lower signal intensity was detected when compared to that observed in the non-normalized cDNA.
A Monte Carlo Markov Chain (MCMC algorithm) was used to generate the predicted probabilities of pathway activity in normalized investigational samples.
Because PCR has its own biases, particularly against large amplicons, we pooled an unamplified, non-normalized sample with a normalized sample in a 1 2 ratio to increase the representation of longer transcripts.
A severe decrease (shift of 11 amplification cycles) in actin relative copy number was measured in the normalized cDNA sample, when compared to the non normalized sample.
We show that the application of such methods in combination with normalization contributed to a substantial reduction of reads representing hemoglobin when compared to the 25.0% hemoglobin reads apparent in the non-normalized sample (B1).
The relative level of mRNA expression in breast cancer cell lines was calculated on the basis of differences in normalized Ct values between samples.
We next used the cumulative Poisson probability distribution (CPPD) to estimate the probability of observing equal or greater read counts in the MeDIP sample than in the same window in the normalized input sample.
Highly expressed genes from non-normalized cDNA, visible as distinct bands on the agarose gel, were absent or greatly reduced in the normalized cDNA sample.
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CEO of Professional Science Editing for Scientists @ prosciediting.com