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Clinical

A module-based translational strategy shows a central role for S100A4 in allergy - GSE46333

Purpose

A generally applicable translational strategy identifies gene signature of allergy.

Hypothesis

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.

Experimental Design

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.

Experimental Variables

siRNA against ELK1, GATA3, NFATC3, MAF, NFKB1, JUN, STAT3 or non-targeting siRNA.

Controls

non-targeting siRNA

Methods

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Additional Information

Questionable signal data; several outliers (by >1000 fold) are presents, not always the same samples.

Microarray
Agilent SurePrint G3 Human GE Probe Name v1
36 Samples Loaded: 36
Human (Homo sapiens)
T cells (CD4+)
Total RNA was extracted using the miRneasy Mini Kit (Qiagen, Valencia,CA, USA).
Sample Set Spreadsheet
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Samples Preview
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
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Quantile Normalized
Raw Signal
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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

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