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Readout of data was a ratio of the gene quantity to its 18S rRNA quantity, defined as relative expression.
Ratios of target gene quantity to each of the three housekeeping gene quantities for each sample were subsequently calculated.
Relative fold change in gene quantity was calculated using naïve resistant mice as a reference.
Since the gene quantity data was derived from the same set of tumors as the expression data, we also tested for a correlation between increased gene quantity and increased mRNA levels.
For matters of consistency with the microarray data, gene expression resulting from qRT-PCR analysis was also calculated as the log2-ratio of normalized gene quantity in elevated pCO2 treated animals to normalized gene quantity in control pCO2 animals.
However, the trends of gene quantity (numbers) and quality (function) in the respective pathways varied between the two time points studied.
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However, often the power of this tool has been limited because primer template mismatches, due to sequence variations of targeted genes, can lead to inaccuracies in measured gene quantities, detection failures, and spurious conclusions.
These raw, not yet normalized, reference gene quantities are the required data input for geNorm.
Sign test was also applied on the experimental vs. control normalized gene quantities of the qRT-PCR.
The number of reads assigned to each KEGG functional category can be used to evaluate gene quantities and expression levels.
Our initial validation step confirmed no difference in reference gene quantities between tumour and normal tissues, allowing subsequent use of NormFinder and geNorm as these models assume that reference genes are not differentially expressed between experimental groups.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com