Comparative analysis of transcriptional profiling of CD3+, CD4+ and CD8+ T cells identifies novel immune response players in T-Cell activation

Additional file 1:

Reproducibility of expression profiles of the T-cell activation in CD3+ cells. Hierarchical clustering (using the Euclidian distance metric) of the 3793 significant genes in T-cell activation of CD3+ cells in three independent biological experiments, E1–E3, (timepoints at 4, 10, 48 and 96 hours) demonstrated high reproducibility. Color denotes degree of differential expression compared to 0 hour (saturated red = 3-fold upregulation, saturated green = 3-fold down-regulation, black = unchanged, gray = no data available).

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Additional file 2:

Complete list of the 3793 significant genes in T-cell activation of CD3+ cells in three independent biological experiments, E1–E3. Color denotes degree of differential expression compared to 0 hour (saturated red = 3-fold upregulation, saturated green = 3-fold down-regulation, black = unchanged, gray = no data available).

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Additional file 3:

Reproducibility of expression profiles of the T-cell activation in CD4+ cells. Hierarchical clustering (using the Euclidian distance metric) of the 1463 significant genes in T-cell activation of CD4+ cells in three independent biological experiments (timepoints at 12, 24, 48 and 72 hours in one experiment, E7; and timepoints at 6, 12, 24, 48 and 72 hours in the other two experiments, E8 and E9) demonstrated high reproducibility. Color denotes degree of differential expression compared to 0 hour (saturated red = 3-fold upregulation, saturated green = 3-fold down-regulation, black = unchanged, gray = no data available).

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Additional file 4:

Complete list of the 1463 significant genes in T-cell activation of CD4+ cells in three independent biological experiments, E7–E9. Color denotes degree of differential expression compared to 0 hour (saturated red = 3-fold upregulation, saturated green = 3-fold down-regulation, black = unchanged, gray = no data available).

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Additional file 5:

Reproducibility of expression profiles of the T-cell activation in CD8+ cells. Hierarchical clustering (using the Euclidian distance metric) of the 1258 significant genes in T-cell activation of CD8+ cells in three independent biological experiments (timepoints at 12, 24, 48 and 72 hours in one experiment, E7; and timepoints at 6, 12, 24, 48 and 72 hours in the other two experiments, E8 and E9) demonstrated high reproducibility. Color denotes degree of differential expression compared to 0 hour (saturated red = 3-fold upregulation, saturated green = 3-fold down-regulation, black = unchanged, gray = no data available).

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Additional file 6:

Complete list of the 1258 significant genes in T-cell activation of CD8+ cells in three independent biological experiments, E7–E9. Color denotes degree of differential expression compared to 0 hour (saturated red = 3-fold upregulation, saturated green = 3-fold down-regulation, black = unchanged, gray = no data available).

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Additional file 7:

The three populations, CD3+, CD4+ and CD8+ T cells, shared largely conserved expression patterns for the significant genes, demonstrated by the hierarchical clustering (using the Euclidian distance metric) of the combined 4167 significant genes upon T-cell activation in CD3+, CD4+ and CD8+ T-cell populations (average of three biological-replicate experiments for each population). Color denotes degree of differential expression comparing to 0 hour (saturated red = 3-fold upregulation, saturated green = 3-fold down-regulation, black = unchanged, gray = no data available).

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Additional file 8:

Complete list of the combined 4167 significant genes upon T-cell activation in CD3+, CD4+ and CD8+ T-cell populations (average of three biological-replicate experiments for each population). Color denotes degree of differential expression comparing to 0 hour (saturated red = 3-fold upregulation, saturated green = 3-fold down-regulation, black = unchanged, gray = no data available).

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Additional file 9:

Q-RT-PCR validation of microarray results across multiple culture samples. (A) Q-RT-PCR versus microarray log expression ratios (timepoint vs. 0 hour) from CD3+ T-cell activation experiments, E1–E3, (for all 12 (= 3 × 4) timepoints: 4, 10, 48 and 96 hours of 3 experiments) for each of the 8 selected genes (FOS, MYB, JUN, CAT, MAPK6, SORD, SOD2, and STAT1). (B) Q-RT-PCR versus microarray log expression ratios (timepoint vs. 0 hour) from CD4+ and CD8+ T-cell activation experiments, E8 and E9, (for all 20 (= 2 × 2 × 5) timepoints: 6, 12, 24, 48 and 72 hours of 2 experiments) for each of the 7 selected genes (EGR1, EGR2, EGR3, FASL, GZMA, GZMB, and MYB).

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