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Comparative transcriptomic analysis of BA- or BL-

GSE13061 Mus musculus (mouse) Expression microarray 20 samples Submitted 2011/01/27 Platform GPL1261
At a glance

Expression microarray · mouse · 20 samples

What it is
Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism
Mus musculus (mouse)
Samples
20 samples: 9 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.
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
This dataset
Open GSE13061 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 (GSE13061_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 PRJNA109981. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21270894) ↗
Study design
9 conditions, mostly in duplicate
colonic epithelium_BA-infection_day7 ×3 colonic epithelium_BL-infection_day7 ×3 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 +1 more

Supports a between-group comparison across 20 samples.

How we read this: 9 replicated groups read from 20 sample titles; they account for 20 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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