Sample Set Annotation Tool: * COD1: A Transcriptomic Reporter Assay Employing Neutrophils to Measure Immunogenic Activity of Septic Patients Plasma GSE49755

Study Design
Assay
Sample Info
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Samples
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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

Controls

uninfected controls (N=12)

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

Sepsis

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	Gender	!Sample_title	cell type	severity	Experiment
GSM1206498	Male	H2-PMN-HC6	neutrophil	-	I
GSM1206499	Female	H1-PMN-Ot3	neutrophil	Severe	I
GSM1206500	Male	H2-PMN-Bp6	neutrophil	Severe	I
GSM1206501	Male	H1-PMN-HC1	neutrophil	-	I
GSM1206502	Female	H2-PMN-Ot3	neutrophil	Severe	I

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

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