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Sample PSP1 showed a somewhat longer post mortem delay than the average of our samples (8.55 hours; average for samples 5 15 hours); however RNA quality, noise levels and the number of detected probes on the microarrays did not differ form other samples (see Table S4[A and B]).
Here we found that eukaryotic elongation factor-2 (eEF-2) was dramatically dephosphorylated within 0.5 2 hr in the hippocampus and amygdala of mice following training in a fear-conditioning test, whereas genome-wide microarrays did not reveal any significant change in the expression level of the mRNAs for translational machineries or their related molecules.
In addition, some tissue samples on tissue microarrays did not adhere to the slide during staining.
However, gene expression was still measured in 1 day intervals, and microarrays did not include all the mouse genes.
Of note, TNF-α expression values obtained by microarrays did not correlate with qPCR performed on un-amplified and un-labelled RNA (not shown).
Using the rt-PCR data as the "ground truth", they found that microarrays did not detect between 24 and 29% of the genes detected by rt-PCR [ 26].
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However, microarrays do not perform well on formalin fixed paraffin embedded tissue (FFPET).
That Affymetrix microarrays do not effectively discriminate between different but closely related duplicated genes has been suggested for allopolyploid wheat [39].
Since Microcebus murinus microarrays do not exist, we decided to use Affymetrix human genome chips since recent studies have illustrated the feasibility of detecting non-human primate brain transcripts using human genome chips [15] [18].
Microarrays do not measure gene expression in absolute units.
In addition, microarrays do not provide quantitative measures, and are therefore not very precise or accurate.
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