Sample Set Annotation Tool: Gene-expression profiling of peripheral blood mononuclear cells in sepsis

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

To identify signature genes that help distinguish (1) sepsis from non-infectious causes of systemic inflammatory response syndrome, (2) between Gram-positive and Gram-negative sepsis.

Hypothesis

Experimental Design

A total of 70 critically ill patients were enrolled in a single-centre observational study. Gene-expression profiling was performed using Affymetrix microarray (U133plus2) with 54,675 transcript. Data was divided into a training set (n=35) and a validation set (n=35). A molecular signature was developed in the training set and was then validated in the validation set.

Experimental Variables

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

Controls

Methods

Affymetrix CEL files were imported into the RMA software (Bioconductor) to compute probeset summaries. Quantile nomalization was used.

Additional Information

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9960

Expected Samples:

70 Samples Loaded: 70

Species

Human (Homo sapiens)

Sample Source

PBMC

Disease

Sepsis

Treatment Protocol

Nil treatment given

Growth Protocol

After each blood sample was collected, mononuclear cells were purified using density gradient separation using Ficoll-Paque (Amersham).

Extraction Protocol

Total RNA extraction using guanidinium thiocyanate (Ambion) according to manufacturer's protocol.

Storage Conditions

Sample Set Spreadsheet

Please log in in order to upload files.

Samples Preview

Sample ID	!Sample Title	group	sepsis
GSM251887	Sepsis gram-positive TP1	Gram-Pos	TRUE
GSM251888	Sepsis gram-positive TP2	Gram-Pos	TRUE
GSM251889	Sepsis gram-positive TP3	Gram-Pos	TRUE
GSM251890	Sepsis gram-positive TP4	Gram-Pos	TRUE
GSM251891	Sepsis gram-positive TP5	Gram-Pos	TRUE

Please log in in order to upload files.

File
sampleset4000181_sampleannotations.csv Sample Set Spreadsheet
sampleset4000181_sampleannotations.csv Sample Set Spreadsheet
sampleset4000181_sampleannotations.csv Sample Set Spreadsheet
sampleset4000181_sampleannotations.csv Sample Set Spreadsheet

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	Sepsis	Control	Gram-Negative	Gram-Positive	Mixed Infection	Type
GSM251887	Sepsis gram-positive TP1	Gram-Pos	TRUE			TRUE		Sepsis
GSM251888	Sepsis gram-positive TP2	Gram-Pos	TRUE			TRUE		Sepsis
GSM251889	Sepsis gram-positive TP3	Gram-Pos	TRUE			TRUE		Sepsis
GSM251890	Sepsis gram-positive TP4	Gram-Pos	TRUE			TRUE		Sepsis
GSM251891	Sepsis gram-positive TP5	Gram-Pos	TRUE			TRUE		Sepsis
GSM251892	Sepsis gram-positive TP6	Gram-Pos	TRUE			TRUE		Sepsis
GSM251893	Sepsis gram-positive TP7	Gram-Pos	TRUE			TRUE		Sepsis
GSM251894	Sepsis gram-positive TP8	Gram-Pos	TRUE			TRUE		Sepsis
GSM251895	Sepsis gram-positive TP9	Gram-Pos	TRUE			TRUE		Sepsis
GSM251896	Sepsis gram-positive TP10	Gram-Pos	TRUE			TRUE		Sepsis
GSM251897	Sepsis gram-negative TN1	Gram-Neg	TRUE		TRUE			Sepsis
GSM251898	Sepsis gram-negative TN2	Gram-Neg	TRUE		TRUE			Sepsis
GSM251899	Sepsis gram-negative TN3	Gram-Neg	TRUE		TRUE			Sepsis
GSM251900	Sepsis gram-negative TN4	Gram-Neg	TRUE		TRUE			Sepsis
GSM251901	Sepsis gram-negative TN5	Gram-Neg	TRUE		TRUE			Sepsis
GSM251902	Sepsis gram-negative TN6	Gram-Neg	TRUE		TRUE			Sepsis
GSM251903	Sepsis gram-negative TN7	Gram-Neg	TRUE		TRUE			Sepsis
GSM251904	Sepsis gram-negative TN8	Gram-Neg	TRUE		TRUE			Sepsis
GSM251905	Sepsis gram-negative TN9	Gram-Neg	TRUE		TRUE			Sepsis
GSM251928	Sepsis mixed infection TM1	Mixed Infection	TRUE				TRUE	Sepsis
GSM251929	Sepsis mixed infection TM2	Mixed Infection	TRUE				TRUE	Sepsis
GSM251930	Sepsis mixed infection TM3	Mixed Infection	TRUE				TRUE	Sepsis
GSM251931	Sepsis mixed infection TM4	Mixed Infection	TRUE				TRUE	Sepsis
GSM251932	Sepsis mixed infection TM5	Mixed Infection	TRUE				TRUE	Sepsis
GSM251933	Sepsis mixed infection TM6	Mixed Infection	TRUE				TRUE	Sepsis
GSM251934	Control TC1	Control		TRUE				Control or SIRS
GSM251935	Control TC2	Control		TRUE				Control or SIRS
GSM251936	Control TC3	Control		TRUE				Control or SIRS
GSM251937	Control TC4	Control		TRUE				Control or SIRS
GSM251938	Control TC5	Control		TRUE				Control or SIRS
GSM251939	Control TC6	Control		TRUE				Control or SIRS
GSM251940	Control TC7	Control		TRUE				Control or SIRS
GSM251941	Control TC8	Control		TRUE				Control or SIRS
GSM251942	Control TC9	Control		TRUE				Control or SIRS
GSM251943	Control TC10	Control		TRUE				Control or SIRS
GSM251944	Sepsis V1	Sepsis	TRUE					Sepsis
GSM251945	Control V2	Control		TRUE				Control or SIRS
GSM251946	Control V3	Control		TRUE				Control or SIRS
GSM251947	Sepsis gram-positive V4	Gram-Pos	TRUE			TRUE		Sepsis
GSM251948	Sepsis gram-positive V5	Gram-Pos	TRUE			TRUE		Sepsis
GSM251949	Sepsis V6	Sepsis	TRUE					Sepsis
GSM251950	Control V7	Control		TRUE				Control or SIRS
GSM251951	Sepsis gram-negative V8	Gram-Neg	TRUE		TRUE			Sepsis
GSM251952	Control V9	Control		TRUE				Control or SIRS
GSM251953	Sepsis mixed infection V10	Mixed Infection	TRUE				TRUE	Sepsis
GSM251982	Sepsis gram-negative V11	Gram-Neg	TRUE		TRUE			Sepsis
GSM251983	Sepsis mixed infection V12	Mixed Infection	TRUE				TRUE	Sepsis
GSM251984	Sepsis mixed infection V13	Mixed Infection	TRUE				TRUE	Sepsis
GSM251985	Sepsis gram-negative V14	Gram-Neg	TRUE		TRUE			Sepsis
GSM251986	Sepsis V15	Sepsis	TRUE					Sepsis
GSM251987	Sepsis gram-negative V16	Gram-Neg	TRUE		TRUE			Sepsis
GSM251988	Sepsis gram-positive V17	Gram-Pos	TRUE			TRUE		Sepsis
GSM251989	Sepsis gram-negative V18	Gram-Neg	TRUE		TRUE			Sepsis
GSM251990	Sepsis gram-negative V19	Gram-Neg	TRUE		TRUE			Sepsis
GSM251991	Sepsis V20	Sepsis	TRUE					Sepsis
GSM251992	Sepsis V21	Sepsis	TRUE					Sepsis
GSM251993	Sepsis gram-negative V22	Gram-Neg	TRUE		TRUE			Sepsis
GSM251994	Control V23	Control		TRUE				Control or SIRS
GSM251995	Sepsis mixed infection V24	Mixed Infection	TRUE				TRUE	Sepsis
GSM251996	Sepsis gram-positive V25	Gram-Pos	TRUE			TRUE		Sepsis
GSM251997	Control V26	Control		TRUE				Control or SIRS
GSM251998	Sepsis V27	Sepsis	TRUE					Sepsis
GSM251999	Sepsis V28	Sepsis	TRUE					Sepsis
GSM252000	Sepsis gram-negative V29	Gram-Neg	TRUE		TRUE			Sepsis
GSM252001	Sepsis gram-positive V30	Gram-Pos	TRUE			TRUE		Sepsis
GSM252002	Sepsis V31	Sepsis	TRUE					Sepsis
GSM252003	Sepsis gram-positive V32	Gram-Pos	TRUE			TRUE		Sepsis
GSM252004	Sepsis gram-positive V33	Gram-Pos	TRUE			TRUE		Sepsis
GSM252005	Sepsis gram-negative V34	Gram-Neg	TRUE		TRUE			Sepsis
GSM252006	Sepsis V35	Sepsis	TRUE					Sepsis

Group Sets View in Gene Expression Browser

Name
All Samples		View
Sepsis Type	Default	View
In order to make new Group Sets or change settings, please log in.

Module Analysis

Group Set
All Samples
Sepsis Type

SIDRA