To verify the aging-induced gene expression alterations in prostate stroma, we performed an additional microarray experiment from laser captured microdissected adjacent stroma from an independent set of 4 month-old (n = 12) and 24 month-old (n = 12) C57BL/6 mice and used a more comprehensive microarray platform comprised of oligonucleotides complementary to ∼40,000 genes.
To measure gene expression variation from the acclimatized colonies in the common garden, a cDNA microarray platform comprised of 8,386 unigenes developed in collaboration by two coral genomics research groups from the Australian National University and James Cook University [ 40] was used.
The microarray platform also comprised 5028 probes for 1875 intragenic elements referred to as "gene-int" (e.g. slr0898-int1), probes for 1939 asRNAs transcribed from the complementary strand of protein-coding genes and referred to as "gene-as" (e.g. sll0247-as), as well as probes for 608 sRNAs originating from intergenic regions, referred to as "NC-X" (e.g. NC-1).
A total of 15,809 expression features were available from 25 studies, utilizing 10 different microarray platforms, and comprising a total of 2,744 patient samples (Table 1).
Importantly, although the gene signature for the AC1 and AC2 subgroups was derived from initial analysis of a small cohort comprising only nine never-smokers, it was successfully validated across much larger AC data sets, e.g., the DCC (n = 349), profiled by different microarray platforms and comprising in total 687 AC tumor cases.
Microarray data from Affymetrix platform comprised of a total of 593 experiments including 11 187 arrays from nine different plant species were used in the current version of PlantRGS.
The third island platform comprises platforms 9 to 12 and also dates from the 1930s.
Affymetrix GPL570 platform comprises approximately 54000 probes, while Illumina platform comprises ~22000 probesets.
This indicates that 95% of the transcripts in the 44 K microarray platform could be validated by mRNA-Seq.
