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Clinical

COD1A: A Transcriptomic Reporter Assay Employing Neutrophils to Measure Immunogenic Activity of Septic Patients Plasma - Neutrophils, experiment I - GSE49755

Purpose

to assess the immunogenicity of plasma from septic patients and evaluate its potential for biomarker discovery

Hypothesis

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Experimental Design

Polymorphonuclear neutrophils (PMNs) were isolated from two healthy donors. Plasma samples were obtained from patients with culture-confirmed sepsis (n=12) and from uninfected controls (n=12). PMNs were cultured for 6 hours in medium alone, plasma from patients with sepsis, plasma from uninfected controls, and LPS using a final concentration of 20%. Transcriptional profiles were acquired using Illumina HumanHT12 V4 BeadChips.

Experimental Variables

Septic Plasma Exposure (2021 ICD-10-CM code* = Not Applicable)

Controls

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Methods

The data were preprocessed using R, which included the following steps: quantile normalization, flooring all intensities <10 to 10, log2 transformation, and PALO (present at least once) filter. PALO, which selects only transcripts with detection p-values < 0.01 in at least one sample, was performed to reduce background noise.

Additional Information

Part of the SuperSeries, GSE49758, "A Transcriptomic Reporter Assay Employing Neutrophils to Measure Immunogenic Activity of Septic Patients' Plasma".

Microarray
Illumina HumanHT-12 v4
40 Samples Loaded: 40
Human (Homo sapiens)
Neutrophils
Septic Plasma Exposure
RNA was extracted using the QIAGEN MicroRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyser.
Sample Set Spreadsheet
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Samples Preview
Sample ID !Sample Title Gender Cell type activators experiment
GSM1206498 H2-PMN-HC6 Male neutrophil Uninfected plasma I
GSM1206499 H1-PMN-Ot3 Female neutrophil Septic plasma I
GSM1206500 H2-PMN-Bp6 Male neutrophil Septic plasma I
GSM1206501 H1-PMN-HC1 Male neutrophil Uninfected plasma I
GSM1206502 H2-PMN-Ot3 Female neutrophil Septic plasma I
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File
sampleset4000072_sampleannotations_v1.csv
Sample Set Spreadsheet
sampleset4000072_sampleannotations_v1.csv
Sample Set Spreadsheet
Log2 Transformed
Raw Signal
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Clinical Datasource
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Samples Viewer / Editor

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Sample ID !Sample Title Gender Cell type Activators Experiment Donors Severity Age (years) Bacterial identification Day of blood collection Sample id
GSM1206498
H2-PMN-HC6
Male
neutrophil
Uninfected plasma
I
H2
-
56
-
 
HC6
GSM1206499
H1-PMN-Ot3
Female
neutrophil
Septic plasma
I
H1
Severe
54
Enterococus faecium
0
Ot3
GSM1206500
H2-PMN-Bp6
Male
neutrophil
Septic plasma
I
H2
Severe
44
Burkholderia pseudomallei
4
Bp6
GSM1206501
H1-PMN-HC1
Male
neutrophil
Uninfected plasma
I
H1
-
59
-
 
HC1
GSM1206502
H2-PMN-Ot3
Female
neutrophil
Septic plasma
I
H2
Severe
54
Enterococus faecium
0
Ot3
GSM1206503
H1-PMN-Ot6
Female
neutrophil
Septic plasma
I
H1
Severe
70
Escherichia coli (ESBL)
30
Ot6
GSM1206504
H2-PMN-HC4
Female
neutrophil
Uninfected plasma
I
H2
-
64
-
 
HC4
GSM1206505
H1-PMN-M1
-
neutrophil
Medium alone
I
H1
-
 
-
 
M1
GSM1206506
H2-PMN-M1
-
neutrophil
Medium alone
I
H2
-
 
-
 
M1
GSM1206507
H1-PMN-Ot1
Male
neutrophil
Septic plasma
I
H1
Severe
24
Streptococcus pnumoniae
0
Ot1
GSM1206508
H2-PMN-LPS1
-
neutrophil
LPS
I
H2
-
 
-
 
LPS
GSM1206509
H1-PMN-Bp6
Male
neutrophil
Septic plasma
I
H1
Severe
44
Burkholderia pseudomallei
4
Bp6
GSM1206510
H2-PMN-Ot6
Female
neutrophil
Septic plasma
I
H2
Severe
70
Escherichia coli (ESBL)
30
Ot6
GSM1206511
H1-PMN-HC4
Female
neutrophil
Uninfected plasma
I
H1
-
64
-
 
HC4
GSM1206512
H2-PMN-Bp5
Male
neutrophil
Septic plasma
I
H2
Non-severe
85
Burkholderia pseudomallei
3
Bp5
GSM1206513
H1-PMN-Ot4
Female
neutrophil
Septic plasma
I
H1
Severe
74
Klebsiella pneumoniae
1
Ot4
GSM1206514
H1-PMN-Bp4
Male
neutrophil
Septic plasma
I
H1
Severe
66
Burkholderia pseudomallei
3
Bp4
GSM1206515
H2-PMN-HC2
Male
neutrophil
Uninfected plasma
I
H2
-
60
-
 
HC2
GSM1206516
H1-PMN-HC5
Male
neutrophil
Uninfected plasma
I
H1
-
56
-
 
HC5
GSM1206517
H1-PMN-Bp2
Male
neutrophil
Septic plasma
I
H1
Severe
50
Burkholderia pseudomallei
22
Bp2
GSM1206518
H2-PMN-Bp1
Male
neutrophil
Septic plasma
I
H2
Severe
57
Burkholderia pseudomallei
1
Bp1
GSM1206519
H2-PMN-HC5
Male
neutrophil
Uninfected plasma
I
H2
-
56
-
 
HC5
GSM1206520
H1-PMN-Bp1
Male
neutrophil
Septic plasma
I
H1
Severe
57
Burkholderia pseudomallei
1
Bp1
GSM1206521
H1-PMN-Bp5
Male
neutrophil
Septic plasma
I
H1
Non-severe
85
Burkholderia pseudomallei
3
Bp5
GSM1206522
H2-PMN-Ot1
Male
neutrophil
Septic plasma
I
H2
Severe
24
Streptococcus pnumoniae
0
Ot1
GSM1206523
H2-PMN-Bp2
Male
neutrophil
Septic plasma
I
H2
Severe
50
Burkholderia pseudomallei
22
Bp2
GSM1206524
H1-PMN-LPS1
-
neutrophil
LPS
I
H1
-
 
-
 
LPS
GSM1206525
H2-PMN-Bp4
Male
neutrophil
Septic plasma
I
H2
Severe
66
Burkholderia pseudomallei
3
Bp4
GSM1206526
H1-PMN-Bp3
Male
neutrophil
Septic plasma
I
H1
Severe
72
Burkholderia pseudomallei
2
Bp3
GSM1206527
H2-PMN-HC3
Female
neutrophil
Uninfected plasma
I
H2
-
57
-
 
HC3
GSM1206528
H1-PMN-HC6
Male
neutrophil
Uninfected plasma
I
H1
-
56
-
 
HC6
GSM1206529
H2-PMN-HC1
Male
neutrophil
Uninfected plasma
I
H2
-
59
-
 
HC1
GSM1206530
H1-PMN-Ot2
Female
neutrophil
Septic plasma
I
H1
Severe
60
Streptococcus pnumoniae
0
Ot2
GSM1206531
H2-PMN-Bp3
Male
neutrophil
Septic plasma
I
H2
Severe
72
Burkholderia pseudomallei
2
Bp3
GSM1206532
H1-PMN-HC3
Female
neutrophil
Uninfected plasma
I
H1
-
57
-
 
HC3
GSM1206533
H2-PMN-Ot4
Female
neutrophil
Septic plasma
I
H2
Severe
74
Klebsiella pneumoniae
1
Ot4
GSM1206534
H1-PMN-Ot5
Female
neutrophil
Septic plasma
I
H1
Severe
77
Pseudomonas aeruginosa
0
Ot5
GSM1206535
H2-PMN-Ot5
Female
neutrophil
Septic plasma
I
H2
Severe
77
Pseudomonas aeruginosa
0
Ot5
GSM1206536
H1-PMN-HC2
Male
neutrophil
Uninfected plasma
I
H1
-
60
-
 
HC2
GSM1206537
H2-PMN-Ot2
Female
neutrophil
Septic plasma
I
H2
Severe
60
Streptococcus pnumoniae
0
Ot2

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