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Clinical

Pediatric septic shock - GSE8121

Purpose

In an ongoing translational research program involving microarray-based expression profiles in pediatric septic shock, we have now conducted longitudinal studies focused on the temporal expression profiles of canonical signaling pathways and gene networks. Genome-level expression profiles were generated from whole blood-derived RNA samples of children with septic shock (n = 30 individual patients) corresponding to days 1 and 3 of admission to the pediatric intensive care unit. Based on sequential statistical and expression filters, day 1 and day 3 of septic shock were characterized by differential regulation of 2,142 and 2,504 gene probes, respectively, relative to normal control patients. Venn analysis demonstrated 239 unique genes in the day 1 data set, 598 unique genes in the day 3 data set, and 1,906 genes common to both data sets. Analyses targeted toward derivation of biological function from these data sets demonstrated time-dependent, differential regulation of genes involved in multiple canonical signaling pathways and gene networks primarily related to immunity and inflammation. Notably, multiple and distinct gene networks involving T cell- and MHC antigen-related biological processes were persistently downregulated from day 1 to day 3. Further analyses demonstrated large scale and persistent downregulation of genes corresponding to functional annotations related to zinc homeostasis. These data represent the largest reported cohort of patients with septic shock, which has undergone longitudinal genome-level expression profiling. The data further advance our genome-level understanding of pediatric septic shock and support novel hypotheses that can be readily tested at both the experimental and translational levels.

Hypothesis

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Experimental Design

To define the longitudinal, genome-level expression profile of children with septic shock.

Experimental Variables

Septic shock (2021 ICD-10-CM code* = R65.21)

Controls

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Methods

The image file was captured on an Affymetrix GeneChip Scanner 3000 and initially processed with Microarray suite 5.0 (Affymetrix).Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.Each array was normalized the same. Global scaling is used by adjusting the average intensity or signal value of each probe array to the same Target Intensity Value (TGV) of 1500. Genechip Operating Software 1v4 (Affymetrix) was then used to generate CEL files from each experiment, which were then imported into GeneSpring for all further data analysis.GeneSpring 7.2 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. All the samples were then normalized to the median of the controls.

Additional Information

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE8121

Microarray
Affymetrix HG-U133_Plus_2
75 Samples Loaded: 75
Human (Homo sapiens)
Whole Blood
Septic Shock
Samples were not manipulated.
Sample Set Spreadsheet
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Samples Preview
Sample ID !Sample Title group All days_Grouping
GSM201230 15_0005_Control_Day1_16 Control Control
GSM201231 15_0003_Control_Day1_19 Control Control
GSM201232 15_0002_Control_Day1_20 Control Control
GSM201233 15_0001_Control_Day1_21 Control Control
GSM201234 11_0037_Control_Day1_25 Control Control
Please log in in order to upload files.
File
sampleset4000187_sampleannotations (1).csv
Sample Set Spreadsheet
sampleset4000187_sampleannotations.csv
Sample Set Spreadsheet
sampleset4000187_sampleannotations_GSE8121_new.csv
Sample Set Spreadsheet
sampleset4000187_sampleannotations_GSE8121_new.csv
Sample Set Spreadsheet
sampleset4000187_sampleannotations_GSE8121_new.csv
Sample Set Spreadsheet
sampleset4000187_sampleannotations_v1.csv
Sample Set Spreadsheet
Raw Signal
Raw Signal
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Links

Samples Viewer / Editor

All fields are editable except the "Sample ID" column. To edit a cell, click within the cell. To edit a "date" cell, click on the calendar icon. To cancel an edit, press the ESC key.

Sample ID !Sample Title Group All days Grouping
GSM201230
15_0005_Control_Day1_16
Control
Control
GSM201231
15_0003_Control_Day1_19
Control
Control
GSM201232
15_0002_Control_Day1_20
Control
Control
GSM201233
15_0001_Control_Day1_21
Control
Control
GSM201234
11_0037_Control_Day1_25
Control
Control
GSM201235
11_0027_Control_Day1_31
Control
Control
GSM201236
11_0020_Control_Day1_37
Control
Control
GSM201237
11_0019_Control_Day1_38
Control
Control
GSM201238
11_0018_Control_Day1_39
Control
Control
GSM201239
11_0014_Control_Day1_46
Control
Control
GSM201240
11_0013_Control_Day1_47
Control
Control
GSM201241
11_0012_Control_Day1_48
Control
Control
GSM201242
11_0011_Control_Day1_49
Control
Control
GSM201243
11_0009_Control_Day1_51
Control
Control
GSM201244
11_0008_Control_Day1_52
Control
Control
GSM201245
05_0007_SepticShock_Day1_3
Septic Shock Day 1
Septic Shock
GSM201246
27_70603_SepticShock_Day1_6
Septic Shock Day 1
Septic Shock
GSM201247
04_0004_SepticShock_Day1_10
Septic Shock Day 1
Septic Shock
GSM201248
15_0008_SepticShock_Day1_13
Septic Shock Day 1
Septic Shock
GSM201249
15_0007_SepticShock_Day1_15
Septic Shock Day 1
Septic Shock
GSM201250
15_0004_SepticShock_Day1_18
Septic Shock Day 1
Septic Shock
GSM201251
11_0029_SepticShock_Day1_30
Septic Shock Day 1
Septic Shock
GSM201252
11_0017_SepticShock_Day1_41
Septic Shock Day 1
Septic Shock
GSM201253
11_0001_SepticShock_Day1_56
Septic Shock Day 1
Septic Shock
GSM201254
10_0020_SepticShock_Day1_57
Septic Shock Day 1
Septic Shock
GSM201255
10_0017_SepticShock_Day1_60
Septic Shock Day 1
Septic Shock
GSM201256
10_0012_SepticShock_Day1_64
Septic Shock Day 1
Septic Shock
GSM201257
10_0004_SepticShock_Day1_73
Septic Shock Day 1
Septic Shock
GSM201258
09_0002_SepticShock_Day1_76
Septic Shock Day 1
Septic Shock
GSM201259
09_0001_SepticShock_Day1_78
Septic Shock Day 1
Septic Shock
GSM201260
07_0002_SepticShock_Day1_82
Septic Shock Day 1
Septic Shock
GSM201261
06_0006_SepticShock_Day1_85
Septic Shock Day 1
Septic Shock
GSM201262
06_0004_SepticShock_Day1_87
Septic Shock Day 1
Septic Shock
GSM201263
06_0003_SepticShock_Day1_89
Septic Shock Day 1
Septic Shock
GSM201264
06_0001_SepticShock_Day1_92
Septic Shock Day 1
Septic Shock
GSM201265
05_0010_SepticShock_Day1_95
Septic Shock Day 1
Septic Shock
GSM201266
05_0008_SepticShock_Day1_97
Septic Shock Day 1
Septic Shock
GSM201267
05_0006_SepticShock_Day1_99
Septic Shock Day 1
Septic Shock
GSM201268
04_0003_SepticShock_Day1_105
Septic Shock Day 1
Septic Shock
GSM201269
02_0001_SepticShock_Day1_108
Septic Shock Day 1
Septic Shock
GSM201270
01_0030_SepticShock_Day1_110
Septic Shock Day 1
Septic Shock
GSM201271
01_0026_SepticShock_Day1_114
Septic Shock Day 1
Septic Shock
GSM201272
01_0025_SepticShock_Day1_116
Septic Shock Day 1
Septic Shock
GSM201273
01_0024_SepticShock_Day1_118
Septic Shock Day 1
Septic Shock
GSM201274
01_0019_SepticShock_Day1_120
Septic Shock Day 1
Septic Shock
GSM201275
05_0007_SepticShock_Day3_2
Septic Shock Day 3
Septic Shock
GSM201276
25_70603_SepticShock_Day3_8
Septic Shock Day 3
Septic Shock
GSM201277
04_0004_SepticShock_Day3_9
Septic Shock Day 3
Septic Shock
GSM201278
15_0008_SepticShock_Day3_12
Septic Shock Day 3
Septic Shock
GSM201279
15_0007_SepticShock_Day3_14
Septic Shock Day 3
Septic Shock
GSM201280
15_0004_SepticShock_Day3_17
Septic Shock Day 3
Septic Shock
GSM201281
11_0029_SepticShock_Day3_29
Septic Shock Day 3
Septic Shock
GSM201282
11_0017_SepticShock_Day3_40
Septic Shock Day 3
Septic Shock
GSM201283
11_0001_SepticShock_Day3_55
Septic Shock Day 3
Septic Shock
GSM201284
10_0020_SepticShock_Day3_58
Septic Shock Day 3
Septic Shock
GSM201285
10_0017_SepticShock_Day3_59
Septic Shock Day 3
Septic Shock
GSM201286
10_0012_SepticShock_Day3_63
Septic Shock Day 3
Septic Shock
GSM201287
10_0004_SepticShock_Day3_72
Septic Shock Day 3
Septic Shock
GSM201288
09_0002_SepticShock_Day3_75
Septic Shock Day 3
Septic Shock
GSM201289
09_0001_SepticShock_Day3_77
Septic Shock Day 3
Septic Shock
GSM201290
07_0002_SepticShock_Day3_81
Septic Shock Day 3
Septic Shock
GSM201291
06_0006_SepticShock_Day3_84
Septic Shock Day 3
Septic Shock
GSM201292
06_0004_SepticShock_Day3_86
Septic Shock Day 3
Septic Shock
GSM201293
06_0003_SepticShock_Day3_88
Septic Shock Day 3
Septic Shock
GSM201294
06_0001_SepticShock_Day3_91
Septic Shock Day 3
Septic Shock
GSM201295
05_0010_SepticShock_Day3_94
Septic Shock Day 3
Septic Shock
GSM201296
05_0008_SepticShock_Day3_96
Septic Shock Day 3
Septic Shock
GSM201297
05_0006_SepticShock_Day3_98
Septic Shock Day 3
Septic Shock
GSM201298
04_0003_SepticShock_Day3_104
Septic Shock Day 3
Septic Shock
GSM201299
02_0001_SepticShock_Day3_107
Septic Shock Day 3
Septic Shock
GSM201300
01_0030_SepticShock_Day3_109
Septic Shock Day 3
Septic Shock
GSM201301
01_0026_SepticShock_Day3_113
Septic Shock Day 3
Septic Shock
GSM201302
01_0025_SepticShock_Day3_115
Septic Shock Day 3
Septic Shock
GSM201303
01_0024_SepticShock_Day3_117
Septic Shock Day 3
Septic Shock
GSM201304
01_0019_SepticShock_Day3_121
Septic Shock Day 3
Septic Shock

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