Sample Set Annotation Tool: Transcriptomic profiling of the inflammatory response after trauma - GSE70311 [Systemic Inflammatory Response Syndrome (SIRS), Sepsis]

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

The study was aimed to identify mechanisms linked to complicated courses after severe trauma by a systems biology approach. In severe trauma, overwhelming systemic inflammation can result in adverse events and the development of complications, including sepsis. In a prospective study, RNA samples from circulating leukocytes from patients with multiple injury (injury severity score ? 17) were analyzed for dynamic changes in gene expression over a period of 21 days by whole genome screening. Based on their clinical presentation, patients were divided into two subgroups: patients with secondary sepsis after trauma (n=5) and patients with systemic inflammation without infection (n=5). Expression cluster were defined by correlating gene expression data with clinical outcome parameters. Using unsupervised clustering, patients with systemic inflammation only and patients with sepsis showed a distinct expression pattern and the discrimination of clinical presentation was reflected by clustering of the samples. Explorative gene set analysis revealed robust upregulation of genes related to ‘hemoglobin metabolism/oxygen transport’ and ‘pathogenic E.coli infection’.

Hypothesis

Experimental Design

10 patients with multi-system trauma (ISS ? 17 points) admitted to the Division of Trauma Surgery at the University Hospital Zurich were included. Whole blood from trauma patients was collected within the first 6 h after trauma (day 0) and on days 1, 2, 3, 5, 7, 10, 14, and 21. Total cellular RNA from circulating leukocytes was isolated using PaxGene Blood RNA Kit (PreAnalytix) for transcriptome profiling. RNA from blood of trauma patients was extracted and subjected to microarray analysis for comparison of longitudinal transcriptomic responses of patients. RNA samples of circulating leukocytes covering time points directly after admission (D0) and on the consecutive days (D1-D21) were subject to multifactorial microarray data analysis: Differences in dynamics of transcripts were assessed by contrasting time- and individual-resolved changes for sepsis and systemic inflammation without infection.

Experimental Variables

Systemic inflammatory response syndrome (2021 ICD-10-CM code* = R65.1)

Sepsis (2021 ICD-10-CM code* = A41)

Controls

Methods

Raw data was pre-processed using GenomeStudio (v 1.9.0). Robust spline normalization (rsn) and detection filtering were performed via the lumi package within Bioconductor and R statistics software (version 3.13). Detection (p<0.01) was required in at least ten samples (out of 90). Candidates were validated by RT-PCR. Annotation was mapped using HumanHT-12_V4_0_R2_15002873_B from Illumina. Analyses were perfomed with respect to individual resolved fold changes (T0-adjusted) as well as global.

Additional Information

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70311

Expected Samples:

90 Samples Loaded: 90

Species

Human (Homo sapiens)

Sample Source

Whole Blood

Disease

Systemic inflammatory response syndrome, Sepsis

Treatment Protocol

High standard protocol.

Growth Protocol

All samples were taken after official registration and written consent.

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	!Sample Title	Gender	Cell type	Grouping	Time point
GSM1723545	P09T00	male	circulating leukocytes	Sepsis	within the first 6 h after trauma (day 0)
GSM1723546	P09T01	male	circulating leukocytes	Sepsis	day 1 after trauma
GSM1723547	P09T02	male	circulating leukocytes	Sepsis	day 2 after trauma
GSM1723548	P09T03	male	circulating leukocytes	Sepsis	day 3 after trauma
GSM1723549	P09T05	male	circulating leukocytes	Sepsis	day 5 after trauma

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File
sampleset4000168_sampleannotations.csv Sample Set Spreadsheet
sampleset4000168_sampleannotations.csv Sample Set Spreadsheet

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Sample ID	!Sample Title	Gender	Cell type	Grouping	Time point	Subject id	Subject status	Subject subgroup
GSM1723545	P09T00	male	circulating leukocytes	Sepsis	within the first 6 h after trauma (day 0)	P09	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723546	P09T01	male	circulating leukocytes	Sepsis	day 1 after trauma	P09	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723547	P09T02	male	circulating leukocytes	Sepsis	day 2 after trauma	P09	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723548	P09T03	male	circulating leukocytes	Sepsis	day 3 after trauma	P09	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723549	P09T05	male	circulating leukocytes	Sepsis	day 5 after trauma	P09	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723550	P09T06	male	circulating leukocytes	Sepsis	day 6 after trauma	P09	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723551	P09T10	male	circulating leukocytes	Sepsis	day 10 after trauma	P09	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723552	P09T14	male	circulating leukocytes	Sepsis	day 14 after trauma	P09	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723553	P09T21	male	circulating leukocytes	Sepsis	day 21 after trauma	P09	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723554	P09T26	male	circulating leukocytes	Sepsis	day 26 after trauma	P09	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723555	P16T00	female	circulating leukocytes	Sepsis	within the first 6 h after trauma (day 0)	P16	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723556	P16T01	female	circulating leukocytes	Sepsis	day 1 after trauma	P16	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723557	P16T02	female	circulating leukocytes	Sepsis	day 2 after trauma	P16	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723558	P16T03	female	circulating leukocytes	Sepsis	day 3 after trauma	P16	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723559	P16T05	female	circulating leukocytes	Sepsis	day 5 after trauma	P16	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723560	P16T07	female	circulating leukocytes	Sepsis	day 7 after trauma	P16	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723561	P16T10	female	circulating leukocytes	Sepsis	day 10 after trauma	P16	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723562	P16T14	female	circulating leukocytes	Sepsis	day 14 after trauma	P16	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723563	P16T21	female	circulating leukocytes	Sepsis	day 21 after trauma	P16	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723564	P16T28	female	circulating leukocytes	Sepsis	day 28 after trauma	P16	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723565	P17T00	male	circulating leukocytes	Systemic Inflammation	within the first 6 h after trauma (day 0)	P17	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723566	P17T01	male	circulating leukocytes	Systemic Inflammation	day 1 after trauma	P17	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723567	P17T02	male	circulating leukocytes	Systemic Inflammation	day 2 after trauma	P17	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723568	P17T03	male	circulating leukocytes	Systemic Inflammation	day 3 after trauma	P17	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723569	P17T05	male	circulating leukocytes	Systemic Inflammation	day 5 after trauma	P17	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723570	P17T07	male	circulating leukocytes	Systemic Inflammation	day 7 after trauma	P17	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723571	P17T10	male	circulating leukocytes	Systemic Inflammation	day 10 after trauma	P17	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723572	P17T14	male	circulating leukocytes	Systemic Inflammation	day 14 after trauma	P17	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723573	P17T21	male	circulating leukocytes	Systemic Inflammation	day 21 after trauma	P17	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723574	P19T00	male	circulating leukocytes	Systemic Inflammation	within the first 6 h after trauma (day 0)	P19	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723575	P19T01	male	circulating leukocytes	Systemic Inflammation	day 1 after trauma	P19	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723576	P19T02	male	circulating leukocytes	Systemic Inflammation	day 2 after trauma	P19	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723577	P19T03	male	circulating leukocytes	Systemic Inflammation	day 3 after trauma	P19	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723578	P19T05	male	circulating leukocytes	Systemic Inflammation	day 5 after trauma	P19	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723579	P19T07	male	circulating leukocytes	Systemic Inflammation	day 7 after trauma	P19	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723580	P19T10	male	circulating leukocytes	Systemic Inflammation	day 10 after trauma	P19	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723581	P19T14	male	circulating leukocytes	Systemic Inflammation	day 14 after trauma	P19	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723582	P19T21	male	circulating leukocytes	Systemic Inflammation	day 21 after trauma	P19	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723583	P34T00	female	circulating leukocytes	Systemic Inflammation	within the first 6 h after trauma (day 0)	P34	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723584	P34T01	female	circulating leukocytes	Systemic Inflammation	day 1 after trauma	P34	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723585	P34T02	female	circulating leukocytes	Systemic Inflammation	day 2 after trauma	P34	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723586	P34T03	female	circulating leukocytes	Systemic Inflammation	day 3 after trauma	P34	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723587	P34T05	female	circulating leukocytes	Systemic Inflammation	day 5 after trauma	P34	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723588	P34T07	female	circulating leukocytes	Systemic Inflammation	day 7 after trauma	P34	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723589	P34T10	female	circulating leukocytes	Systemic Inflammation	day 10 after trauma	P34	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723590	P34T14	female	circulating leukocytes	Systemic Inflammation	day 14 after trauma	P34	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723591	P34T21	female	circulating leukocytes	Systemic Inflammation	day 21 after trauma	P34	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723592	P35T00	male	circulating leukocytes	Systemic Inflammation	within the first 6 h after trauma (day 0)	P35	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723593	P35T01	male	circulating leukocytes	Systemic Inflammation	day 1 after trauma	P35	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723594	P35T02	male	circulating leukocytes	Systemic Inflammation	day 2 after trauma	P35	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723595	P35T03	male	circulating leukocytes	Systemic Inflammation	day 3 after trauma	P35	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723596	P35T05	male	circulating leukocytes	Systemic Inflammation	day 5 after trauma	P35	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723597	P35T07	male	circulating leukocytes	Systemic Inflammation	day 7 after trauma	P35	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723598	P35T10	male	circulating leukocytes	Systemic Inflammation	day 10 after trauma	P35	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723599	P35T14	male	circulating leukocytes	Systemic Inflammation	day 14 after trauma	P35	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723600	P36T00	male	circulating leukocytes	Sepsis	within the first 6 h after trauma (day 0)	P36	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723601	P36T01	male	circulating leukocytes	Sepsis	day 1 after trauma	P36	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723602	P36T02	male	circulating leukocytes	Sepsis	day 2 after trauma	P36	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723603	P36T03	male	circulating leukocytes	Sepsis	day 3 after trauma	P36	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723604	P36T05	male	circulating leukocytes	Sepsis	day 5 after trauma	P36	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723605	P36T07	male	circulating leukocytes	Sepsis	day 7 after trauma	P36	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723606	P36T10	male	circulating leukocytes	Sepsis	day 10 after trauma	P36	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723607	P36T14	male	circulating leukocytes	Sepsis	day 14 after trauma	P36	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723608	P36T21	male	circulating leukocytes	Sepsis	day 21 after trauma	P36	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723609	P42T00	male	circulating leukocytes	Sepsis	within the first 6 h after trauma (day 0)	P42	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723610	P42T01	male	circulating leukocytes	Sepsis	day 1 after trauma	P42	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723611	P42T02	male	circulating leukocytes	Sepsis	day 2 after trauma	P42	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723612	P42T03	male	circulating leukocytes	Sepsis	day 3 after trauma	P42	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723613	P42T05	male	circulating leukocytes	Sepsis	day 5 after trauma	P42	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723614	P42T07	male	circulating leukocytes	Sepsis	day 7 after trauma	P42	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723615	P42T10	male	circulating leukocytes	Sepsis	day 10 after trauma	P42	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723616	P42T14	male	circulating leukocytes	Sepsis	day 14 after trauma	P42	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723617	P42T21	male	circulating leukocytes	Sepsis	day 21 after trauma	P42	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723618	P43T00	male	circulating leukocytes	Systemic Inflammation	within the first 6 h after trauma (day 0)	P43	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723619	P43T01	male	circulating leukocytes	Systemic Inflammation	day 1 after trauma	P43	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723620	P43T02	male	circulating leukocytes	Systemic Inflammation	day 2 after trauma	P43	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723621	P43T03	male	circulating leukocytes	Systemic Inflammation	day 3 after trauma	P43	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723622	P43T05	male	circulating leukocytes	Systemic Inflammation	day 5 after trauma	P43	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723623	P43T07	male	circulating leukocytes	Systemic Inflammation	day 7 after trauma	P43	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723624	P43T10	male	circulating leukocytes	Systemic Inflammation	day 10 after trauma	P43	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723625	P43T14	male	circulating leukocytes	Systemic Inflammation	day 14 after trauma	P43	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723626	P43T21	male	circulating leukocytes	Systemic Inflammation	day 21 after trauma	P43	patients with multi-system trauma (ISS ≥ 17 points)	patients with systemic inflammation without infection
GSM1723627	P47T00	male	circulating leukocytes	Sepsis	within the first 6 h after trauma (day 0)	P47	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723628	P47T01	male	circulating leukocytes	Sepsis	day 1 after trauma	P47	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723629	P47T03	male	circulating leukocytes	Sepsis	day 3 after trauma	P47	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723630	P47T05	male	circulating leukocytes	Sepsis	day 5 after trauma	P47	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723631	P47T07	male	circulating leukocytes	Sepsis	day 7 after trauma	P47	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723632	P47T10	male	circulating leukocytes	Sepsis	day 10 after trauma	P47	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723633	P47T14	male	circulating leukocytes	Sepsis	day 14 after trauma	P47	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma
GSM1723634	P47T21	male	circulating leukocytes	Sepsis	day 21 after trauma	P47	patients with multi-system trauma (ISS ≥ 17 points)	patients with secondary sepsis after trauma

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