Sample Set Annotation Tool: Tracking the molecular patterns of a common response across tissues in murine sepsis to refine treatment strategies

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Transcriptional effects in liver, lung, spleen and blood samples from mice challenged to Sham and Sepsis by Peritoneal Contamination and Infection (PCI) were monitored after 6 and 24 hours.

Hypothesis

Experimental Design

4 Tissues x 2 Time Resolved Treatment Groups x 4 Replicates, 4 Tissues x Sham Control x 3 Replicates.

Experimental Variables

Controls

Methods

Gene chips from 44 samples (four tissues; four replicates for 6 h and 24 h post-infection and three replicates sham) were scanned and pre-processed using BeadStudio (version 3.23). Data analysis was carried out using R statistics software (version 2.92) and BioConductor (version 2.3). A robust spline normalization, combining the features of quantile and loess normalization, was conducted for the tissue separated sample groups (liver, lung, spleen and blood) and log 2 signals were obtained.

Additional Information

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23767

Expected Samples:

44 Samples Loaded: 44

Species

Mouse (Mus musculus)

Sample Source

Spleen , Whole Blood , Lung , Liver

Disease

Sepsis

Treatment Protocol

1. faecal Peritonitis: intraperitoneal injection of 200µl of a human faeces suspension (KBE 75 x 10^6/ml), 2. Sham controls: intraperitoneal injection of 200µl of physiological sodium chloride.

Growth Protocol

8 weeks old female C57/BL6 Jackson mice.

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

Please log in in order to upload files.

Samples Preview

Sample ID	!Sample Title	Grouping	Sex	strain	Age (weeks)
GSM586668	T1-S1-R1	liver samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586669	T1-S1-R2	liver samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586670	T1-S1-R3	liver samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586671	T1-S2-R1	liver samples from mice challenged to PCI treatment monitored after 6 hours	female	C57/BL6	8
GSM586672	T1-S2-R2	liver samples from mice challenged to PCI treatment monitored after 6 hours	female	C57/BL6	8

Please log in in order to upload files.

File
sampleset4000232_sampleannotations.csv Sample Set Spreadsheet
sampleset4000232_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	Grouping	Sex	Strain	Age (weeks)
GSM586668	T1-S1-R1	liver samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586669	T1-S1-R2	liver samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586670	T1-S1-R3	liver samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586671	T1-S2-R1	liver samples from mice challenged to PCI treatment monitored after 6 hours	female	C57/BL6	8
GSM586672	T1-S2-R2	liver samples from mice challenged to PCI treatment monitored after 6 hours	female	C57/BL6	8
GSM586673	T1-S2-R3	liver samples from mice challenged to PCI treatment monitored after 6 hours	female	C57/BL6	8
GSM586674	T1-S2-R4	liver samples from mice challenged to PCI treatment monitored after 6 hours	female	C57/BL6	8
GSM586675	T1-S3-R1	liver samples from mice challenged to PCI treatment monitored after 24 hours	female	C57/BL6	8
GSM586676	T1-S3-R2	liver samples from mice challenged to PCI treatment monitored after 24 hours	female	C57/BL6	8
GSM586677	T1-S3-R3	liver samples from mice challenged to PCI treatment monitored after 24 hours	female	C57/BL6	8
GSM586678	T1-S3-R4	liver samples from mice challenged to PCI treatment monitored after 24 hours	female	C57/BL6	8
GSM586679	T2-S1-R1	lung samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586680	T2-S1-R2	lung samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586681	T2-S1-R3	lung samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586682	T2-S2-R1	lung samples from mice challenged to PCI treatment monitored after 6 hours	female	C57/BL6	8
GSM586683	T2-S2-R2	lung samples from mice challenged to PCI treatment monitored after 6 hours	female	C57/BL6	8
GSM586684	T2-S2-R3	lung samples from mice challenged to PCI treatment monitored after 6 hours	female	C57/BL6	8
GSM586685	T2-S2-R4	lung samples from mice challenged to PCI treatment monitored after 6 hours	female	C57/BL6	8
GSM586686	T2-S3-R1	lung samples from mice challenged to PCI treatment monitored after 24 hours	female	C57/BL6	8
GSM586687	T2-S3-R2	lung samples from mice challenged to PCI treatment monitored after 24 hours	female	C57/BL6	8
GSM586688	T2-S3-R3	lung samples from mice challenged to PCI treatment monitored after 24 hours	female	C57/BL6	8
GSM586689	T2-S3-R4	lung samples from mice challenged to PCI treatment monitored after 24 hours	female	C57/BL6	8
GSM586690	T3-S1-R1	spleen samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586691	T3-S1-R2	spleen samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586692	T3-S1-R3	spleen samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586693	T3-S2-R1	spleen samples from mice challenged to PCI treatment monitored after 6 hours	female	C57/BL6	8
GSM586694	T3-S2-R2	spleen samples from mice challenged to PCI treatment monitored after 6 hours	female	C57/BL6	8
GSM586695	T3-S2-R3	spleen samples from mice challenged to PCI treatment monitored after 6 hours	female	C57/BL6	8
GSM586696	T3-S2-R4	spleen samples from mice challenged to PCI treatment monitored after 6 hours	female	C57/BL6	8
GSM586697	T3-S3-R1	spleen samples from mice challenged to PCI treatment monitored after 24 hours	female	C57/BL6	8
GSM586698	T3-S3-R2	spleen samples from mice challenged to PCI treatment monitored after 24 hours	female	C57/BL6	8
GSM586699	T3-S3-R3	spleen samples from mice challenged to PCI treatment monitored after 24 hours	female	C57/BL6	8
GSM586700	T3-S3-R4	spleen samples from mice challenged to PCI treatment monitored after 24 hours	female	C57/BL6	8
GSM586701	T4-S1-R1	blood samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586702	T4-S1-R2	blood samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586703	T4-S1-R3	blood samples from mice challenged to sham treatment	female	C57/BL6	8
GSM586704	T4-S2-R1	blood samples from mice challenged to PCI treatment were monitored after 6 hours	female	C57/BL6	8
GSM586705	T4-S2-R2	blood samples from mice challenged to PCI treatment were monitored after 6 hours	female	C57/BL6	8
GSM586706	T4-S2-R3	blood samples from mice challenged to PCI treatment were monitored after 6 hours	female	C57/BL6	8
GSM586707	T4-S2-R4	blood samples from mice challenged to PCI treatment were monitored after 6 hours	female	C57/BL6	8
GSM586708	T4-S3-R1	blood samples from mice challenged to PCI treatment were monitored after 24 hours	female	C57/BL6	8
GSM586709	T4-S3-R2	blood samples from mice challenged to PCI treatment were monitored after 24 hours	female	C57/BL6	8
GSM586710	T4-S3-R3	blood samples from mice challenged to PCI treatment were monitored after 24 hours	female	C57/BL6	8
GSM586711	T4-S3-R4	blood samples from mice challenged to PCI treatment were monitored after 24 hours	female	C57/BL6	8

Group Sets View in Gene Expression Browser

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

Module Analysis

Group Set
All Samples
Treatment

SIDRA