It is known that in most samples and conditions genome-wide microarrays include a large proportion of the genes that are not expressed and therefore they give signal close to the background or noise.
Chlamydia suis was demonstrated in most samples and overall, no correlation to clinical signs was detected.
All miRNAs including RNU6B showed reliable Ct values in most samples, and fluorescent signals failed to reach the set threshold after 40 cycles in very few assays.
For most samples and analyses 65 82 % of genes were within scaffolds but only 19 48 % were within SNP haplotypes despite the greater length of SNP haplotypes.
Expression varied, possibly owing to variable efficiency of RNA extraction, but VEGF165b was seen in most samples and VEGF165 in some.
All the assayed SNPs amplified in most samples and only 12 were monomorphic in all the accessions genotyped, giving a validation ratio of 92%.
Housekeeping genes like G3PDH or β actin are used because they are abundant in most samples and show little variation between experiments.
We observed similar levels of expression for most sPLA2s in left and right normal mucosa, with PLA2G2A having a high expression level, PLA2G3 being not detectable in most samples and the other sPLA2 genes showing intermediate levels of expression.
This issue was more pronounced in CCS levels 3 and 4. Using the most granular CCS code available for each ICD-9 code in the universal CCS did not improve results in most samples and the full cohort.
Also, the three angiogenesis-related genes, ANGPTL4, VEGFA and ESM1, seem to be expressed at their original levels in most samples and have altered expression in only a few samples.
