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Microarray data were validated by real time PCR in a set of nine genes showing a high degree of correlation.
All genes showing a two fold or greater change across the various fractions are listed in Table S1 and S2.
The genes showing a strain by stage interaction display significant enrichment of genes that have been implicated in innate immunity (p = .00215).00215
Hence, the number of genes showing a significant difference in gene expression between ESCs and iPSCs in most tested comparisons is low.
An Excel list of all significant genes showing a <2% false discovery rate is included for the reader as a supplemental file (Dataset S1).
Up regulated genes (265) were as frequent as down-regulated ones (251), with 27 genes showing a fold change greater than 5-fold (supplementary data S4).
GO enrichment analysis of genes showing a pattern of interest was carried out with a Chi-square test with Yates continuity correction [12].
Each sample from one group was compared with each sample from the other group, and only genes showing a fold change ≥1.8 between groups were retained.
The first 8 hours following synchronization by thymidine release represent one complete cycle with >98% of the 2,833 cyclic genes showing a clear peak during this period.
We find that the correlation between RNA-seq data and microarray data is dependent on the gene length, with longer genes showing a better correlation.
We focused on those genes showing a FC ≥ 2.0.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com