Sample Set Annotation Tool: A Transcriptomic Reporter Assay Employing Neutrophils to Measure Immunogenic Activity of Septic Patients Plasma - Neutrophils, experiment I

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

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

Hypothesis

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

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".

Expected Samples:

40 Samples Loaded: 40

Species

Human (Homo sapiens)

Sample Source

Neutrophils

Disease

Septic Plasma Exposure

Treatment Protocol

Growth Protocol

Extraction Protocol

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.

Storage Conditions

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

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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