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IL-22 plays an indispensable role in early host defense against attaching and effacing (A/E) bacterial pathogens

GSE10010 Mus musculus (mouse) Expression microarray 6 samples Submitted 2008/02/11 Platform GPL2872

At a glance

Expression microarray · mouse · 6 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Mus musculus (mouse)
Samples: 6 samples: 3 × colon_control vs 3 × colon_il22Groups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Infection by attaching and effacing (A/E) pathogens poses a serious threat to public health, as was highlighted by the recent outbreak of E. coli O157:H7 infection in the United States. Here, by using a murine A/E pathogen, Citrobacter rodentium, we demonstrate that C. rodentium infection is lethal to IL-22-/- mice within two weeks. IL-22, in the early phase of infection, is indispensable for preventing the invasion of bacteria through the intestinal epithelium, and thereby preventing systemic spread and mortality.

Read the full summary ↓

We also show that IL-23 is required for the early induction of IL-22 during C. rodentium infection. Finally, our data suggest that IL-22 exerts its function by boosting the innate immune responses of colonic epithelial cells, especially though the induction of anti-microbial proteins, RegIIIβ and RegIIIγ. Keywords: treatment comparison

This dataset

Open GSE10010 in finder → Find more mouse microarray datasets →

Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE10010_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA108197. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 18264109) ↗

Study design

3 × colon_control vs 3 × colon_il22

Supports a between-group comparison across 6 samples.

How we read this: 2 replicated groups read from 6 sample titles; they account for 6 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM252890 colon_control_rep1 colon_control
GSM252931 colon_control_rep2 colon_control
GSM252932 colon_control_rep3 colon_control
GSM252933 colon_il22_rep1 colon_il22
GSM252934 colon_il22_rep2 colon_il22
GSM252935 colon_il22_rep3 colon_il22

Datasets on a similar topic

GSE236344 IL-33 controls IL-22-dependent antibacterial defense by modulating the microbiota. 80 samples shares il-22, bacterial, defense
GSE236342 IL-33 controls IL-22-dependent antibacterial defense by modulating the microbiota [scRNA-seq] 8 samples shares il-22, bacterial, defense
GSE236341 IL-33 controls IL-22-dependent antibacterial defense by modulating the microbiota [bulk RNA-seq] 7 samples shares il-22, bacterial, defense
GSE206534 Characterization of the host defense against influenza virus infection and a secondary bacterial pneumonia infection 51 samples shares bacterial, defense, against
GSE292930 Proton-activated chloride channel 1 is essential for innate host defense against bacterial sepsis 24 samples shares bacterial, defense, against
GSE248348 A Th17 cell-intrinsic glutathione/mitochondrial-IL-22 axis protects against intestinal inflammation 9 samples shares il-22, against
GSE227331 T cell-derived IL-22 directs mature colonocyte fate and upregulates host defense genes during Citrobacter rodentium infection. 6 samples shares il-22, defense
GSE328526 Eosinophil-derived COX-2 protects against experimental colitis through the PGE2–IL-22 axis 4 samples shares il-22, against

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