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Gene expression patterns in house dust mite stimulated CD4 T cells and IgG to IgE ratios - GSE70760

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Clinical

Gene expression patterns in house dust mite stimulated CD4 T cells and IgG to IgE ratios - GSE70760

Purpose

Distinguishing benign from pathologic TH2 immunity in atopic children

Hypothesis

HDM generate a distinct transcriptomic signature in CD4 T cells.

Experimental Design

The study design consisted of 45 subjects and two conditions (medium control, HDM stimulation).

Experimental Variables

Stimulation with HDM

Controls

Stimulation with AIM-V medium alone.

Methods

PBMC from house dust mite (HDM) sensitized atopics were cultured in the presence or absence of HDM extract for 24 hours. At the termination of the cultures, CD4 T cells were isolated using immunomagnetic separation. Gene expression was profiled on microarrays.

Additional Information

The microarray data was preprocessed in R employing the RMA algorithm and a custom chip description file (hugene10st_Hs_ENTREZG, v19). ComBat was used to adjust the data for batch effects.

Microarray
Affymetrix HuGene-1_0-st (hugene10st_Hs_ENT) v1
90 Samples Loaded: 90
Human (Homo sapiens)
PBMC , T cells (CD4+)
Allergy
PBMC were cultured in medium alone or in the presence of HDM extract (10 ug/ml).
PBMC were cultured in AIM-V medium.
Total RNA was extracted employing TRIzol followed by RNeasy.
Sample Set Spreadsheet
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Samples Preview
Sample ID !Sample Title Stimulation IgG_IgE ratio
GSM1817497 HDM sensitized atopic subject # AA01 medium control Control 15.9373804
GSM1817498 HDM sensitized atopic subject # AA01 HDM stimulated HDM 15.9373804
GSM1817499 HDM sensitized atopic subject # AA03 medium control Control 72.9559159
GSM1817500 HDM sensitized atopic subject # AA03 HDM stimulated HDM 72.9559159
GSM1817501 HDM sensitized atopic subject # AA08 medium control Control 5.82710383

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File
gse70760_sampleannotations_v1.csv
Sample Set Spreadsheet
gse70760_sampleannotations_v1.csv
Sample Set Spreadsheet
sampleset4000091_sampleannotationsv2.csv
Sample Set Spreadsheet
sampleset4000091_sampleannotationsv2.csv
Sample Set Spreadsheet
Log2 Transformed
Raw Signal
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Clinical Datasource
Links
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70760
https://www.ncbi.nlm.nih.gov/pubmed/26518094

Samples Viewer / Editor

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Sample ID !Sample Title Stimulation IgG IgE ratio
GSM1817497
HDM sensitized atopic subject # AA01 medium control
Control
15.9373804
GSM1817498
HDM sensitized atopic subject # AA01 HDM stimulated
HDM
15.9373804
GSM1817499
HDM sensitized atopic subject # AA03 medium control
Control
72.9559159
GSM1817500
HDM sensitized atopic subject # AA03 HDM stimulated
HDM
72.9559159
GSM1817501
HDM sensitized atopic subject # AA08 medium control
Control
5.82710383
GSM1817502
HDM sensitized atopic subject # AA08 HDM stimulated
HDM
5.82710383
GSM1817503
HDM sensitized atopic subject # AA09 medium control
Control
13.837984
GSM1817504
HDM sensitized atopic subject # AA09 HDM stimulated
HDM
13.837984
GSM1817505
HDM sensitized atopic subject # AA11 medium control
Control
0.773467108
GSM1817506
HDM sensitized atopic subject # AA11 HDM stimulated
HDM
0.773467108
GSM1817507
HDM sensitized atopic subject # AA12 medium control
Control
16.5415008
GSM1817508
HDM sensitized atopic subject # AA12 HDM stimulated
HDM
16.5415008
GSM1817509
HDM sensitized atopic subject # AA15 medium control
Control
17.7489229
GSM1817510
HDM sensitized atopic subject # AA15 HDM stimulated
HDM
17.7489229
GSM1817511
HDM sensitized atopic subject # AA16 medium control
Control
2.24345653
GSM1817512
HDM sensitized atopic subject # AA16 HDM stimulated
HDM
2.24345653
GSM1817513
HDM sensitized atopic subject # AA18 medium control
Control
10.4205652
GSM1817514
HDM sensitized atopic subject # AA18 HDM stimulated
HDM
10.4205652
GSM1817515
HDM sensitized atopic subject # AA19 medium control
Control
25.3241558
GSM1817516
HDM sensitized atopic subject # AA19 HDM stimulated
HDM
25.3241558
GSM1817517
HDM sensitized atopic subject # AA20 medium control
Control
2.5911201
GSM1817518
HDM sensitized atopic subject # AA20 HDM stimulated
HDM
2.5911201
GSM1817519
HDM sensitized atopic subject # AA21 medium control
Control
13.9421911
GSM1817520
HDM sensitized atopic subject # AA21 HDM stimulated
HDM
13.9421911
GSM1817521
HDM sensitized atopic subject # AA22 medium control
Control
5.55477397
GSM1817522
HDM sensitized atopic subject # AA22 HDM stimulated
HDM
5.55477397
GSM1817523
HDM sensitized atopic subject # AA23 medium control
Control
2.5052011
GSM1817524
HDM sensitized atopic subject # AA23 HDM stimulated
HDM
2.5052011
GSM1817525
HDM sensitized atopic subject # AA24 medium control
Control
12.4420953
GSM1817526
HDM sensitized atopic subject # AA24 HDM stimulated
HDM
12.4420953
GSM1817527
HDM sensitized atopic subject # AA25 medium control
Control
26.0085287
GSM1817528
HDM sensitized atopic subject # AA25 HDM stimulated
HDM
26.0085287
GSM1817529
HDM sensitized atopic subject # AA26 medium control
Control
18.5422824
GSM1817530
HDM sensitized atopic subject # AA26 HDM stimulated
HDM
18.5422824
GSM1817531
HDM sensitized atopic subject # AA27 medium control
Control
194.999779
GSM1817532
HDM sensitized atopic subject # AA27 HDM stimulated
HDM
194.999779
GSM1817533
HDM sensitized atopic subject # AA29 medium control
Control
4.66531751
GSM1817534
HDM sensitized atopic subject # AA29 HDM stimulated
HDM
4.66531751
GSM1817535
HDM sensitized atopic subject # AA30 medium control
Control
8.15202521
GSM1817536
HDM sensitized atopic subject # AA30 HDM stimulated
HDM
8.15202521
GSM1817537
HDM sensitized atopic subject # AA31 medium control
Control
16.4053962
GSM1817538
HDM sensitized atopic subject # AA31 HDM stimulated
HDM
16.4053962
GSM1817539
HDM sensitized atopic subject # AN01 medium control
Control
6.90879359
GSM1817540
HDM sensitized atopic subject # AN01 HDM stimulated
HDM
6.90879359
GSM1817541
HDM sensitized atopic subject # AN02 medium control
Control
92.6311286
GSM1817542
HDM sensitized atopic subject # AN02 HDM stimulated
HDM
92.6311286
GSM1817543
HDM sensitized atopic subject # AN04 medium control
Control
41.9088468
GSM1817544
HDM sensitized atopic subject # AN04 HDM stimulated
HDM
41.9088468
GSM1817545
HDM sensitized atopic subject # AN05 medium control
Control
8.10828938
GSM1817546
HDM sensitized atopic subject # AN05 HDM stimulated
HDM
8.10828938
GSM1817547
HDM sensitized atopic subject # AN06 medium control
Control
16.549158
GSM1817548
HDM sensitized atopic subject # AN06 HDM stimulated
HDM
16.549158
GSM1817549
HDM sensitized atopic subject # AN07 medium control
Control
34.3143083
GSM1817550
HDM sensitized atopic subject # AN07 HDM stimulated
HDM
34.3143083
GSM1817551
HDM sensitized atopic subject # AN11 medium control
Control
11.2601083
GSM1817552
HDM sensitized atopic subject # AN11 HDM stimulated
HDM
11.2601083
GSM1817553
HDM sensitized atopic subject # AN14 medium control
Control
6.17283951
GSM1817554
HDM sensitized atopic subject # AN14 HDM stimulated
HDM
6.17283951
GSM1817555
HDM sensitized atopic subject # AN15 medium control
Control
106.198182
GSM1817556
HDM sensitized atopic subject # AN15 HDM stimulated
HDM
106.198182
GSM1817557
HDM sensitized atopic subject # AN16 medium control
Control
23.8985242
GSM1817558
HDM sensitized atopic subject # AN16 HDM stimulated
HDM
23.8985242
GSM1817559
HDM sensitized atopic subject # AN17 medium control
Control
18.4214817
GSM1817560
HDM sensitized atopic subject # AN17 HDM stimulated
HDM
18.4214817
GSM1817561
HDM sensitized atopic subject # AN19 medium control
Control
220.622971
GSM1817562
HDM sensitized atopic subject # AN19 HDM stimulated
HDM
220.622971
GSM1817563
HDM sensitized atopic subject # AN20 medium control
Control
6.49359168
GSM1817564
HDM sensitized atopic subject # AN20 HDM stimulated
HDM
6.49359168
GSM1817565
HDM sensitized atopic subject # AN21 medium control
Control
29.5438879
GSM1817566
HDM sensitized atopic subject # AN21 HDM stimulated
HDM
29.5438879
GSM1817567
HDM sensitized atopic subject # AN23 medium control
Control
12.8397622
GSM1817568
HDM sensitized atopic subject # AN23 HDM stimulated
HDM
12.8397622
GSM1817569
HDM sensitized atopic subject # AN24 medium control
Control
65.6331064
GSM1817570
HDM sensitized atopic subject # AN24 HDM stimulated
HDM
65.6331064
GSM1817571
HDM sensitized atopic subject # AN25 medium control
Control
3.32809248
GSM1817572
HDM sensitized atopic subject # AN25 HDM stimulated
HDM
3.32809248
GSM1817573
HDM sensitized atopic subject # AN26 medium control
Control
3.04349353
GSM1817574
HDM sensitized atopic subject # AN26 HDM stimulated
HDM
3.04349353
GSM1817575
HDM sensitized atopic subject # AN27 medium control
Control
165.286639
GSM1817576
HDM sensitized atopic subject # AN27 HDM stimulated
HDM
165.286639
GSM1817577
HDM sensitized atopic subject # AN28 medium control
Control
101.883314
GSM1817578
HDM sensitized atopic subject # AN28 HDM stimulated
HDM
101.883314
GSM1817579
HDM sensitized atopic subject # AN29 medium control
Control
11.1688649
GSM1817580
HDM sensitized atopic subject # AN29 HDM stimulated
HDM
11.1688649
GSM1817581
HDM sensitized atopic subject # AN30 medium control
Control
418.897481
GSM1817582
HDM sensitized atopic subject # AN30 HDM stimulated
HDM
418.897481
GSM1817583
HDM sensitized atopic subject # AN31 medium control
Control
7.61324619
GSM1817584
HDM sensitized atopic subject # AN31 HDM stimulated
HDM
7.61324619
GSM1817585
HDM sensitized atopic subject # AN32 medium control
Control
805.832497
GSM1817586
HDM sensitized atopic subject # AN32 HDM stimulated
HDM
805.832497

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