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Comparative transcriptomic analysis of BA- or BL- associated murine colonic epithelium after O157 infection

GSE12998 Mus musculus (mouse) Expression microarray 14 samples Submitted 2011/01/27 Platform GPL1261
At a glance

Expression microarray · mouse · 14 samples

What it is
Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism
Mus musculus (mouse)
Samples
14 samples: 7 conditions, mostly in duplicateGroups 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)
A huge number of microorganisms are colonized in human gut and the balance of their composition is closely related to human health. Recently, many probiotics such as bifidobacteria or lactobacilli have been introduced in our life as effective agents. However, we have not well understood their beneficial mechanisms including host-bacterial crosstalk. Accordingly, we took advantage of the protective mechanisms of probiotics against lethal infection of enterohemorrhagic Escherichia coli O157:H7 in murine gnotobiote model system
This dataset
Open GSE12998 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 (GSE12998_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 PRJNA114253. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21270894) ↗
Study design
7 conditions, mostly in duplicate
colonic epithelium_BA+E-infection_day1 ×2 colonic epithelium_GF ×2 colonic epithelium_E-infection_day1 ×2 colonic epithelium_E-infection_day5 ×2 colonic epithelium_BL+E-infection_day1 ×2 colonic epithelium_BL+E-infection_day7 ×2 colonic epithelium_BA+E-infection_day7 ×2

Supports a between-group comparison across 14 samples.

How we read this: 7 replicated groups read from 14 sample titles; they account for 14 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
Datasets on a similar topic

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