To maximize coverage of the non-coding transcriptome and to confirm that the use of microarray platforms did not bias our analyses of myelopoiesis, we performed RNA-sequencing (RNA-seq) in myeloblasts, promyelocytes, metamyelocytes, and mature neutrophils to represent the myeloid differentiation path23 (Fig. 3b, c).
Overall the two microarray platforms did not reveal a clear correlation between differential CpG methylation and differential mRNA expression in long-term culture or aging (Fig. 4B,C).
An investigation of the probe sequences of the most highly expressed genes in the microarray platforms did not reveal noticeable differences in the number of possible sequence matches between those found in MPSS and those not found in MPSS.
As the HG_U133A microarray platform does not include probes for GITR, FOLR4, and GRP83, the expression of these genes could not be analyzed.
A pathway-based analysis thus can reveal biologically relevant similarity between results of different microarray studies even though the gene contents of the microarray platforms used do not match exactly.
In a broader context, gene expression patterns derived via different methodologies (e.g. qPCR vs. microarray platforms) often do not strongly correlate, although there appears to be more concordance between qPCR and next-generation sequencing platforms than with microarrays (cf. [ 53, 54]), which may relate to overall transcript abundance [ 52].
Profiling on the individual microarray platforms was done according to manufacturer's specifications.
Mapping across microarray platforms was done using the "Cleanex" database [ 14] to retrieve corresponding gene symbols and Affymetrix probe sets.
Third, the Illumina microarray platform, strikingly, did not trend well with the sample titration as the absolute fold-change values that followed the sample titrations were observed in only 5-75-7%f genes.
