GEO series

Human epithelial cell response to bacterial signal indole

GSE14379 Homo sapiens (human) Expression microarray 9 samples Submitted 2009/12/22 Platform GPL8060

At a glance

Expression microarray · human · 9 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 9 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Indole is a bacterial signal secreted by pathogenic and commensal Escherichia coli in the stationary phase at high concentrations (~600 µM). Prior work from our lab has shown that indole decreases E. coli O157:H7 (EHEC) chemotaxis, motility, attachment to epithelial cells and biofilm formation. However, its effect on epithelial cells is not known.

Read the full summary ↓

We hypothesized that indole induces gene expression changes in epithelial cells that lead to decreased pathogen colonization and infection. Changes in gene expression with the human enterocyte cell line HCT-8 exposed to indole suggested down-regulation of Toll-like receptor signaling and coordinated changes in Jak-STAT and p38 MAPK pathways. Corresponding changes in the expression of cytokines, chemokines, and their receptors also suggested that indole functions as a modulator of inflammation in intestinal epithelial cells. In addition, the expression of genes involved in tight junction organization (claudins, and tight junction proteins) and mucin production were also up-regulated by indole. Keywords: Inter-kingdom signaling interactions between human cells and bacterial signal indole

This dataset

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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 (GSE14379_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 PRJNA111427. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 19966295) ↗

Samples in this study

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+ 9 more — browse all 9 samples with per-sample file links →

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