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To minimize the effect of failed assays, we merged the three datasets to cover 4,287 genes measured at least once in the three measurements and calculated the total copy number from the average copy number of each of these genes.
To detect the global structure of the data, the expression of the genes measured at both the transcript and protein levels was subjected to hierarchical clustering (Figure S1B).
It contains the expression profiles of more than 6000 yeast genes measured at 17 conditions over two complete cell cycles.
To confirm that the observed deregulated expression of STAT3 target genes among early RA patients was downstream of IL-6 signalling, primary human CD4 T cells were incubated in vitro with recombinant human IL-6 and the expression of relevant target genes measured at 1 and 6 h (see online supplementary text and figures S6 S7).
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It is, perhaps, not surprising that a strong association between birth weight and the expression of any particular gene, measured at a single time point (delivery, in most cases), has proven elusive, even for genes which have mechanistic links to growth.
Then, for each gene we computed the percentiles of the log2 ratios (only for genes measured in at least 300 samples).
Poisson error is lower in genes measured with at least ten reads, which is true for > 95% of our core genes, in all samples used for DE calls.
Levels were also measured after 4 days depuration; however there was no significant difference in mRNA levels for any of the genes measured across the treatments at this time point (i.e., no treatment effects; data not shown).
For validation we compared the expression ratios of six selected genes measured via qRT-PCR at each time point after CRH stimulation with the corresponding expression profiles from the microarray using statistical tests.
Meanwhile, the gene expression levels of PAMP-associated genes were measured at 2, 3, 4, and 8 dpi.
Free auxin and expression of auxin-related genes were measured at ripening in MADS8 suppressed apple fruit.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com