A module-based translational strategy shows a central role for S100A4 in allergy - GSE46333
A generally applicable translational strategy identifies gene signature of allergy.
We hypothesized that genes co-regulated with a key gene in allergy, IL13, would form a module that could help to discover novel candidate genes.
Human CD4+ T cells (hBP CD4+ T cells, 2W-200, Lonza, Vallensbak Strand, Denkmark) were nucleofected either with nucleofection buffer, 1 µM human on target plus SMART pool siRNA against ELK1, GATA3, NFATC3, MAF, NFKB1, JUN, STAT3 (Dharmacon, Lafayette, CO) or non-targeting siRNA using the AMAXA nucleofection program U-014. Six hours after then nucleofection cells were washed, activated and polarized towards Th2. The CD4+ cells were activated with plate bound anti-CD3 (500ng / ml for coating of the plate), with soluble anti-CD28 (500ng / ml) and with IL-2 (17ng /ml, all purchased from R&D). Th2 polarization was induced with anti-IL-12 (5µg/ml) and IL-4 (10ng / ml). For RT-PCR and microarray analyisis the cells were harvested 12 hours of polarization and total RNA was extracted.
siRNA against ELK1, GATA3, NFATC3, MAF, NFKB1, JUN, STAT3 or non-targeting siRNA.
non-targeting siRNA
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Questionable signal data; several outliers (by >1000 fold) are presents, not always the same samples.
Sample ID | !Sample_title | tissue | cell type | sirna |
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GSM1128702 | Control_replicate_1 | whole blood | CD4+ T cells | scramble |
GSM1128703 | Control_replicate_2 | whole blood | CD4+ T cells | scramble |
GSM1128704 | Control_replicate_3 | whole blood | CD4+ T cells | scramble |
GSM1128705 | Control_replicate_4 | whole blood | CD4+ T cells | scramble |
GSM1128706 | Control_replicate_5 | whole blood | CD4+ T cells | scramble |
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Sample ID | !Sample Title | Tissue | Cell type | Sirna |
---|---|---|---|---|
GSM1128702 | Control_replicate_1 |
whole blood |
CD4+ T cells |
scramble |
GSM1128703 | Control_replicate_2 |
whole blood |
CD4+ T cells |
scramble |
GSM1128704 | Control_replicate_3 |
whole blood |
CD4+ T cells |
scramble |
GSM1128705 | Control_replicate_4 |
whole blood |
CD4+ T cells |
scramble |
GSM1128706 | Control_replicate_5 |
whole blood |
CD4+ T cells |
scramble |
GSM1128707 | Control_replicate_6 |
whole blood |
CD4+ T cells |
scramble |
GSM1128708 | Control_replicate_7 |
whole blood |
CD4+ T cells |
scramble |
GSM1128709 | Control_replicate_8 |
whole blood |
CD4+ T cells |
scramble |
GSM1128710 | ELK1 knockdown_1 |
whole blood |
CD4+ T cells |
ELK1 |
GSM1128711 | ELK1 knockdown_2 |
whole blood |
CD4+ T cells |
ELK1 |
GSM1128712 | ELK1 knockdown_3 |
whole blood |
CD4+ T cells |
ELK1 |
GSM1128713 | ELK1 knockdown_4 |
whole blood |
CD4+ T cells |
ELK1 |
GSM1128714 | GATA3 Knockdown_1 |
whole blood |
CD4+ T cells |
GATA3 |
GSM1128715 | GATA3 Knockdown_2 |
whole blood |
CD4+ T cells |
GATA3 |
GSM1128716 | GATA3 Knockdown_3 |
whole blood |
CD4+ T cells |
GATA3 |
GSM1128717 | GATA3 Knockdown_4 |
whole blood |
CD4+ T cells |
GATA3 |
GSM1128718 | JUN Knockdown_1 |
whole blood |
CD4+ T cells |
JUN |
GSM1128719 | JUN Knockdown_2 |
whole blood |
CD4+ T cells |
JUN |
GSM1128720 | JUN Knockdown_3 |
whole blood |
CD4+ T cells |
JUN |
GSM1128721 | JUN Knockdown_4 |
whole blood |
CD4+ T cells |
JUN |
GSM1128722 | MAF knockdown_1 |
whole blood |
CD4+ T cells |
MAF |
GSM1128723 | MAF knockdown_2 |
whole blood |
CD4+ T cells |
MAF |
GSM1128724 | MAF knockdown_3 |
whole blood |
CD4+ T cells |
MAF |
GSM1128725 | MAF knockdown_4 |
whole blood |
CD4+ T cells |
MAF |
GSM1128726 | NFATC3 knockdown_1 |
whole blood |
CD4+ T cells |
NFATC3 |
GSM1128727 | NFATC3 knockdown_2 |
whole blood |
CD4+ T cells |
NFATC3 |
GSM1128728 | NFATC3 knockdown_3 |
whole blood |
CD4+ T cells |
NFATC3 |
GSM1128729 | NFATC3 knockdown_4 |
whole blood |
CD4+ T cells |
NFATC3 |
GSM1128730 | NFKB1 knockdown_1 |
whole blood |
CD4+ T cells |
NFKB1 |
GSM1128731 | NFKB1 knockdown_2 |
whole blood |
CD4+ T cells |
NFKB1 |
GSM1128732 | NFKB1 knockdown_3 |
whole blood |
CD4+ T cells |
NFKB1 |
GSM1128733 | NFKB1 knockdown_4 |
whole blood |
CD4+ T cells |
NFKB1 |
GSM1128734 | STAT3 knockdown_1 |
whole blood |
CD4+ T cells |
STAT3 |
GSM1128735 | STAT3 knockdown_2 |
whole blood |
CD4+ T cells |
STAT3 |
GSM1128736 | STAT3 knockdown_3 |
whole blood |
CD4+ T cells |
STAT3 |
GSM1128737 | STAT3 knockdown_4 |
whole blood |
CD4+ T cells |
STAT3 |
Name | ||
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