DNA methylation changes were measured using Array-PRIMES method (aPRIMES) followed by whole-genome hybridization using human DNA methylation promoter microarray NimbleGen HG18 Refseq Promoter 3×720 K array.
The signal intensities of the spots and background values were measured using array vision 7.0 (array vision, USA).
Spot density for each gene was measured using Array-Vision software (Version 5.1, Imaging Research, Canada), along with numerous quality control parameters (compare Array-Vision manual).
However, before being able to determine which probes provided a noisy signal, it was necessary to estimate the expected background noise when comparing methylation measured using array hybridization to methylation measured using bisulfite sequencing.
We examined the correlation of the log ratios between the array platforms and miRNA expression measured using TaqMan arrays, as qRT-PCR is often considered to be the 'gold standard' for validation.
Gene expression was measured using nylon arrays containing the PCR fragments (EUROGENTEC) for all genes of L. lactis IL1403 [ 16].
Gene expression was measured using nylon arrays containing PCR fragments (Eurogentec®) for 1948 genes of L. lactis IL1403.
Therefore, the release of inflammatory mediators from A β- and minocycline-treated astrocyte-enriched cultures was measured using cytokine arrays.
Twenty-five days later, gene expression was measured using Affymetrix arrays and differential expression patterns identified by principal component analysis (see Supporting materials and methods Data S1 for details).
