Genome wide transcriptional analysis of resting and IL2 activated human natural killer cells: gene expression signatures indicative of novel molecular signaling pathways

Additional file 1:

Correlation Coefficient Mapping. Reproducibility of the duplicate hybridization experiments on spotted microarray was checked through correlation coefficient mapping programmed in BRB-ArrayTools. High correlation is seen among technical duplicates from the same samples.

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Additional file 2:

NK signature dervived from oligonucleotide microarray platform. Differentially expressed genes with ≥ 2 fold higher expressions in resting NK cells compared to the lymphoid RNA standard and also ≥ 2 fold higher expression than tonsillar cells and resting CD8⁺ T cells.

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Additional file 3:

NK signature dervived from affymetrix chip platform. The NK cell signature derived from the GeneChipU133plus 2^® was based on similar comparisons as performed in spotted microarray, with the modification that, tonsil profile was replaced with a universal RNA standard (Stratagene Inc, CA).

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Additional file 4:

Common genes in resting NK signature from signature database [17] and our Affymetrix data. NK signature common to our data set and curated signature from the signature database (Shaffer, A.L., et al. Immunol Rev, 210, 67–85, 2006)

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Additional file 5:

SOM representation of the genome wide transcriptional changes upon IL2 stimulation. The NK0 map represent resting NK cells, NK2, NK8 and NK24 maps represent NK cells after 2, 8, or 24 hours of culture with IL2, respectively. Color coding index stands for the expression values of genes so that the brighter the color, the higher the value. Each hexagon in a certain position of the maps contains a group of genes, identified by the SOM algorithm that has very similar expression patterns throughout the time points of the experiment. Differentially expressed genes are illustrated: (A) Early upregulated, (B) Early downregulated, (C) Genes upregulated at 8 hours, (D)Genes downregulated at 8 hours, (E) Late upregulated, (F) Late downregulated, (G) Genes showing continuous increased expression during culture period.

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Additional file 6:

Representative groups of genes or pathways with sufficient expressed common genes for both are presented showing similarty in both formats. The maximum differences in expression levels between resting NK cells and IL2 activated NK cells after 2, 8 or 24 hours for the spotted microarray data are shown. The color change in each row represents the gene expression relative to the median across the samples and values are visualized according to the scale bar that represents the expression fold (log2) relative to median. A) Cytolytic pathway, B) Secretory signature, C) Cell cycle and proliferation, D) Quiescent signature.

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Additional file 7:

Signaling pathways. A) JAK/STAT pathway, B) PI3K-activation pathway, C) I: NF-κB pathway regulation and II: NF-κB target genes. (See also additional file 6 legend for details).

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Additional file 8:

Supplemental Table 2: Donors of NK cells used in the experiments. Purity of the NK cells is indicated in () after the donor ID. Information on donor number and purity of included NK cells.

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