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After 1 h incubation, unincorporated dye was removed using CentriSep spin columns (Princeton Separations, Inc .. Hybridization and detection of microarray signals was performed as described [19].

To compare qPCR-array and microarray assays, the log2 of microarray signals was used.

The microarray signals were analyzed using the Affymetrix RMA algorithm.

Microarray signals were analysed using a rank based statistic, Rank products (RP) [11].

Microarray signals were determined using Affymetrix Microarray Suite 5.1.

Surprisingly, however, microarray signals were lower using the LNA PLP compared with the same PLP without LNA substitutes (Fig.  1).

Microarray signals were normalized to allow comparison of samples with different RNA amounts, using the spike-in data.

In contrast, microarray signals are scanned fluorescence intensities, and this translates into continuous and nearly normal expression data.

Microarray signals were rescaled to co-analyze data from different arrays by equating the average of the spike-specific signals from each microarray.

Since microarray signals are not quantitative at lower and higher values, signal thresholds for floor and ceiling were set for all samples.

For HSP60, HSP70, and HSP100, the expression levels were already high and the microarray signals were almost saturated even under the normal growth conditions (42 °C, pH 2.3).