Rhinovirus-Induced Modulation of Gene Expression in Human Bronchial Epithelial Cells From

Rhinovirus-induced modulation of gene expression in bronchial epithelial cells from subjects with asthma

YA Bochkov, KM Hanson, S Keles, RA Brockman-Schneider, NN Jarjour, and JE Gern

Online supplementary materials

Supplementary Table 1 Comparison of genes up-regulated (≥ 2-fold) in normal and asthmatic PBE cells after RV1A infection.

Supplementary Table 2 Comparison of genes down-regulated (≥ 4-fold) in normal and asthmatic PBE cells after RV1A infection.

Supplementary Table 3 Twenty genes with the greatest up-regulation in either normal or asthmatic PBE cells after RV1A infection (HG Focus genechip).

Supplementary Table 4 Genes revealed differences in expression (≥ 1.5-fold) between asthmatic and normal PBE cells after RV1A infection.

Supplementary Table 5 Reference positions of SYBR Green real-time PCR primers (custom PCR array # CAPH0280, SuperArray) used for microarray data validation.

Supplementary Table 6 SYBR Green real-time PCR primers used for microarray data validation.

Methods

Supplementary Table 1 Comparison of genes up-regulated (≥ 2-fold) in normal and asthmatic PBE cells after RV1A infection.

Abbreviations: NI, normal infected; NM, normal mock-infected; AI, asthma infected, AM, asthma mock-infected.

aThese genes had more than one probe set that revealed similar expression changes; corresponding fold changes and p-values were averaged.

bGene symbols are not available for these probe sets.

cThese genes were selected from AI vs. AM comparison at 2-fold cutoff (adjusted P<0.05).

dThese genes were selected from NI vs. NM comparison at 2-fold cutoff (adjusted P<0.05).

Supplementary Table 2 Comparison of genes down-regulated (≥ 4-fold) in normal and asthmatic PBE cells after RV1A infection.

Abbreviations: NI, normal infected; NM, normal mock-infected; AI, asthma infected, AM, asthma mock-infected.

aGene symbols are not available for these probe sets.

bThese genes had more than one probe set that revealed similar expression changes; corresponding fold changes and p-values were averaged.

cThese genes were selected from NI vs. NM comparison at 4-fold cutoff (adjusted P<0.05).

dThese genes were selected from AI vs. AM comparison at 4-fold cutoff (adjusted P<0.05).

Supplementary Table 3 Twenty genes with the greatest up-regulation in either normal or asthmatic PBE cells after RV1A infection (HG Focus genechip).

Abbreviations: NI, normal infected; NM, normal mock-infected; AI asthmatic infected, AM, asthmatic mock-infected.

aNominal P-values from paired t-test comparisons.

Supplementary Table 4 Genes revealed differences in expression (≥ 1.5-fold) between asthmatic and normal PBE cells after RV1A infection.

aNominal P values from unpaired t-test

bThese genes were either up- or down-regulated after RV1A infection in normal and/or asthmatic cells at 2-fold cutoff.

cThese genes had more than one probe set that revealed similar expression changes; corresponding fold changes and p-values were averaged.

dNegative numbers indicate down-regulation in asthmatic cells.

Supplementary Table 5 Reference positions of SYBR Green real-time PCR primers (custom PCR array # CAPH0280, SuperArray) used for microarray data validation.

Abbreviations: bp, base pairs.

Supplementary Table 6 SYBR Green real-time PCR primers used for microarray data validation.

Abbreviations: f, forward primer; r, reverse primer; bp, base pairs.