Sample Set Annotation Tool: Microarray analysis of human monocytes infected with Francisella tularensis-GSE12108

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

The goal was to examine genomewide transcriptional reponses to these two strains, and identify differentially-regulated genes that may help explain the virulence of Schu S4.

Hypothesis

Experimental Design

Human monocytes were infected with the Schu S4 isolate of Francisella tularensis tularensis (n=4), with F. tularensis subspecies novicida isolate U112 (n=4) or were left uninfected (n=6). Gene expression values were calculated using the gcrma package in R and BioConductor, and limma to identify differentially expressed genes. Submitted here are expression values calculated using R 2.7.1 and BioConductor 2.2 (FreeBSD/amd64) but the original were done using R 2.6.1 and BioConductor 2.1 (FreeBSD/amd64). Twelve other chips were pooled with these 14 for preprocessing.

Experimental Variables

Controls

Methods

Additional Information

Butchar JP, Cremer TJ, Clay CD, Gavrilin MA et al. Microarray analysis of human monocytes infected with Francisella tularensis identifies new targets of host response subversion. PLoS One 2008 Aug 13;3(8):e2924. PMID: 18698339

Expected Samples:

14 Samples Loaded: 14

Species

Human (Homo sapiens)

Sample Source

Monocytes

Disease

Healthy

Treatment Protocol

Growth Protocol

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	!Sample_title	Culture conditions	healthy adult
GSM305429	F. novicida infected D1_FN	F. novicida	True
GSM305430	Uninfected D1_UT	Uninfected	True
GSM305431	F. novicida infected D2_FN	F. novicida	True
GSM305432	Uninfected D2_UT	Uninfected	True
GSM305433	F. novicida infected D3_FN	F. novicida	True

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File
sampleset4000087_sampleannotations.csv Sample Set Spreadsheet

Samples Viewer / Editor

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Sample ID	!Sample Title	Culture conditions	Healthy adult
GSM305429	F. novicida infected D1_FN	F. novicida	True
GSM305430	Uninfected D1_UT	Uninfected	True
GSM305431	F. novicida infected D2_FN	F. novicida	True
GSM305432	Uninfected D2_UT	Uninfected	True
GSM305433	F. novicida infected D3_FN	F. novicida	True
GSM305434	Uninfected D3_UT	Uninfected	True
GSM305435	F. novicida infected D4_FN	F. novicida	True
GSM305436	Uninfected D4_UT	Uninfected	True
GSM305437	Schu S4 infected D5_S4	Schu S4	True
GSM305438	Uninfected D5_UT	Uninfected	True
GSM305439	Schu S4 infected D6_S4	Schu S4	True
GSM305440	Uninfected D6_UT	Uninfected	True
GSM305441	Schu S4 infected D7_S4	Schu S4	True
GSM305442	Schu S4 infected D8_S4	Schu S4	True

Group Sets View in Gene Expression Browser

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Module Analysis

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SIDRA