Sample Set Annotation Tool: Hepatic induction of cholesterol biosynthesis reflects a remote adaptive response to pneumococcal pneumonia

Study Design
Assay
Sample Info
Files
Info
Samples
Group Sets
Analysis

Purpose

Transcriptional effects in liver, lung and blood samples from mice after intratracheal challenge with either Streptococcus pneumoniae serotype 19 (lobar-pneumonia) or serotype 2 (sepsis) were monitored after 6 and 24 hours and compared to sham (vehicle control).We gratefully acknowledge the BMBF grant within the “Promoting global research excellence in severe sepsis” (PROGRESS) study (01KI07111).

Hypothesis

Experimental Design

Three tissues x two serotypes x two time resolved treatment groups x four replicates, three tissues x Sham Control x three replicates.

Experimental Variables

Controls

Methods

Gene chips 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 2.4.1). The arrays were normalized organ-wise using variance stabilising normalisation (Huber et al.).

Additional Information

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26472

Expected Samples:

57 Samples Loaded: 57

Species

Mouse (Mus musculus)

Sample Source

Whole Blood , Liver , Lung

Disease

Sepsis, Streptococcus pneumoniae

Treatment Protocol

Growth Protocol

8 weeks old female C57/BL6 Jackson mice.

Extraction Protocol

Storage Conditions

Sample Set Spreadsheet

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Samples Preview

Sample ID	!Sample Title	Gender	infection	tissue	strain
GSM650993	Liver-S0-T6-R1	Female	sham	Liver	C57/BL6 Jackson
GSM650994	Liver-S0-T6-R2	Female	sham	Liver	C57/BL6 Jackson
GSM650995	Liver-S0-T6-R3	Female	sham	Liver	C57/BL6 Jackson
GSM650996	Liver-S2-T6-R1	Female	Streptococcus pneumoniae serotype 2	Liver	C57/BL6 Jackson
GSM650997	Liver-S2-T6-R2	Female	Streptococcus pneumoniae serotype 2	Liver	C57/BL6 Jackson

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File
sampleset4000233_sampleannotations.csv Sample Set Spreadsheet
sampleset4000233_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	Gender	Infection	Tissue	Strain	Age (weeks)	Infection Tissue Timepoint	Time point (hours)
GSM650993	Liver-S0-T6-R1	Female	sham	Liver	C57/BL6 Jackson	8	Liver_sham
GSM650994	Liver-S0-T6-R2	Female	sham	Liver	C57/BL6 Jackson	8	Liver_sham
GSM650995	Liver-S0-T6-R3	Female	sham	Liver	C57/BL6 Jackson	8	Liver_sham
GSM650996	Liver-S2-T6-R1	Female	Streptococcus pneumoniae serotype 2	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 2_6 hours	6
GSM650997	Liver-S2-T6-R2	Female	Streptococcus pneumoniae serotype 2	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 2_6 hours	6
GSM650998	Liver-S2-T6-R3	Female	Streptococcus pneumoniae serotype 2	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 2_6 hours	6
GSM650999	Liver-S2-T6-R4	Female	Streptococcus pneumoniae serotype 2	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 2_6 hours	6
GSM651000	Liver-S2-T24-R1	Female	Streptococcus pneumoniae serotype 2	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 2_24 hours	24
GSM651001	Liver-S2-T24-R2	Female	Streptococcus pneumoniae serotype 2	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 2_24 hours	24
GSM651002	Liver-S2-T24-R3	Female	Streptococcus pneumoniae serotype 2	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 2_24 hours	24
GSM651003	Liver-S2-T24-R4	Female	Streptococcus pneumoniae serotype 2	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 2_24 hours	24
GSM651004	Liver-S19-T6-R1	Female	Streptococcus pneumoniae serotype 19	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 19_6 hours	6
GSM651005	Liver-S19-T6-R2	Female	Streptococcus pneumoniae serotype 19	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 19_6 hours	6
GSM651006	Liver-S19-T6-R3	Female	Streptococcus pneumoniae serotype 19	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 19_6 hours	6
GSM651007	Liver-S19-T6-R4	Female	Streptococcus pneumoniae serotype 19	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 19_6 hours	6
GSM651008	Liver-S19-T24-R1	Female	Streptococcus pneumoniae serotype 19	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 19_24 hours	24
GSM651009	Liver-S19-T24-R2	Female	Streptococcus pneumoniae serotype 19	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 19_24 hours	24
GSM651010	Liver-S19-T24-R3	Female	Streptococcus pneumoniae serotype 19	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 19_24 hours	24
GSM651011	Liver-S19-T24-R4	Female	Streptococcus pneumoniae serotype 19	Liver	C57/BL6 Jackson	8	Liver_Streptococcus pneumoniae serotype 19_24 hours	24
GSM651012	Lung-S0-T6-R1	Female	sham	Lung	C57/BL6 Jackson	8	Lung_sham
GSM651013	Lung-S0-T6-R2	Female	sham	Lung	C57/BL6 Jackson	8	Lung_sham
GSM651014	Lung-S0-T6-R3	Female	sham	Lung	C57/BL6 Jackson	8	Lung_sham
GSM651015	Lung-S2-T6-R1	Female	Streptococcus pneumoniae serotype 2	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 2_6 hours	6
GSM651016	Lung-S2-T6-R2	Female	Streptococcus pneumoniae serotype 2	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 2_6 hours	6
GSM651017	Lung-S2-T6-R3	Female	Streptococcus pneumoniae serotype 2	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 2_6 hours	6
GSM651018	Lung-S2-T6-R4	Female	Streptococcus pneumoniae serotype 2	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 2_6 hours	6
GSM651019	Lung-S2-T24-R1	Female	Streptococcus pneumoniae serotype 2	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 2_24 hours	24
GSM651020	Lung-S2-T24-R2	Female	Streptococcus pneumoniae serotype 2	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 2_24 hours	24
GSM651021	Lung-S2-T24-R3	Female	Streptococcus pneumoniae serotype 2	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 2_24 hours	24
GSM651022	Lung-S2-T24-R4	Female	Streptococcus pneumoniae serotype 2	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 2_24 hours	24
GSM651023	Lung-S19-T6-R1	Female	Streptococcus pneumoniae serotype 19	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 19_6 hours	6
GSM651024	Lung-S19-T6-R2	Female	Streptococcus pneumoniae serotype 19	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 19_6 hours	6
GSM651025	Lung-S19-T6-R3	Female	Streptococcus pneumoniae serotype 19	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 19_6 hours	6
GSM651026	Lung-S19-T6-R4	Female	Streptococcus pneumoniae serotype 19	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 19_6 hours	6
GSM651027	Lung-S19-T24-R1	Female	Streptococcus pneumoniae serotype 19	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 19_24 hours	24
GSM651028	Lung-S19-T24-R2	Female	Streptococcus pneumoniae serotype 19	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 19_24 hours	24
GSM651029	Lung-S19-T24-R3	Female	Streptococcus pneumoniae serotype 19	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 19_24 hours	24
GSM651030	Lung-S19-T24-R4	Female	Streptococcus pneumoniae serotype 19	Lung	C57/BL6 Jackson	8	Lung_Streptococcus pneumoniae serotype 19_24 hours	24
GSM651031	Blood-S0-T6-R1	Female	sham	Blood	C57/BL6 Jackson	8	Blood_sham
GSM651032	Blood-S0-T6-R2	Female	sham	Blood	C57/BL6 Jackson	8	Blood_sham
GSM651033	Blood-S0-T6-R3	Female	sham	Blood	C57/BL6 Jackson	8	Blood_sham
GSM651034	Blood-S2-T6-R1	Female	Streptococcus pneumoniae serotype 2	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 2_6 hours	6
GSM651035	Blood-S2-T6-R2	Female	Streptococcus pneumoniae serotype 2	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 2_6 hours	6
GSM651036	Blood-S2-T6-R3	Female	Streptococcus pneumoniae serotype 2	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 2_6 hours	6
GSM651037	Blood-S2-T6-R4	Female	Streptococcus pneumoniae serotype 2	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 2_6 hours	6
GSM651038	Blood-S2-T24-R1	Female	Streptococcus pneumoniae serotype 2	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 2_24 hours	24
GSM651039	Blood-S2-T24-R2	Female	Streptococcus pneumoniae serotype 2	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 2_24 hours	24
GSM651040	Blood-S2-T24-R3	Female	Streptococcus pneumoniae serotype 2	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 2_24 hours	24
GSM651041	Blood-S2-T24-R4	Female	Streptococcus pneumoniae serotype 2	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 2_24 hours	24
GSM651042	Blood-S19-T6-R1	Female	Streptococcus pneumoniae serotype 19	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 19_6 hours	6
GSM651043	Blood-S19-T6-R2	Female	Streptococcus pneumoniae serotype 19	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 19_6 hours	6
GSM651044	Blood-S19-T6-R3	Female	Streptococcus pneumoniae serotype 19	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 19_6 hours	6
GSM651045	Blood-S19-T6-R4	Female	Streptococcus pneumoniae serotype 19	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 19_6 hours	6
GSM651046	Blood-S19-T24-R1	Female	Streptococcus pneumoniae serotype 19	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 19_24 hours	24
GSM651047	Blood-S19-T24-R2	Female	Streptococcus pneumoniae serotype 19	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 19_24 hours	24
GSM651048	Blood-S19-T24-R3	Female	Streptococcus pneumoniae serotype 19	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 19_24 hours	24
GSM651049	Blood-S19-T24-R4	Female	Streptococcus pneumoniae serotype 19	Blood	C57/BL6 Jackson	8	Blood_Streptococcus pneumoniae serotype 19_24 hours	24

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