GEO series

Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip

GSE65790 Homo sapiens (human) Expression microarray 6 samples Submitted 2015/12/16 Platform GPL6244

At a glance

Expression microarray · human · 6 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 6 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

A human gut-on-a-chip microdevice was used to coculture multiple commensal microbes in contact with living human intestinal epithelial cells for more than a week in vitro and to analyze how gut microbiome, inflammatory cells, and peristalsis-associated mechanical deformations independently contribute to intestinal bacterial overgrowth and inflammation.

Read the full summary ↓

This in vitro model replicated results from past animal and human studies, including demonstration that probiotic and antibiotic therapies can suppress villus injury induced by pathogenic bacteria. By ceasing peristalsis-like motions while maintaining luminal flow, lack of epithelial deformation was shown to trigger bacterial overgrowth similar to that observed in patients with ileus and inflammatory bowel disease. Analysis of intestinal inflammation on-chip revealed that immune cells and lipopolysaccharide endotoxin together stimulate epithelial cells to produce four proinflammatory cytokines (IL-8, IL-6, IL-1β, and TNF-α) that are necessary and sufficient to induce villus injury and compromise intestinal barrier function. Thus, this human gut-on-a-chip can be used to analyze contributions of microbiome to intestinal pathophysiology and dissect disease mechanisms in a controlled manner that is not possible using existing in vitro systems or animal models.

This dataset

Open GSE65790 in finder → Find more human 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 (GSE65790_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 PRJNA275063. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 26668389) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 6 more — browse all 6 samples with per-sample file links →

Datasets on a similar topic

GSE168018 Impaired antibacterial immune signaling and changes in the lung microbiome precedes secondary bacterial pneumonia in COVID-19 (scRNA-seq) 19 samples shares microbiome, bacterial
GSE234357 Multimodal immune cell phenotyping in gastrointestinal biopsies reveals microbiome-related T cell modulations in human GvHD patients 18 samples shares microbiome, intestinal
GSE81279 Alterations of the human gut microbiome in multiple sclerosis 72 samples shares microbiome
GSE316497 Genotype-Epigenome-Phenotype Integration Reveals the Contributions of Peripheral Immune Cells to Bipolar Disorder Pathogenesis, Phenotypic Heterogeneity, and Therapy 1012 samples shares contributions
GSE314923 Immune-microbiome coordination defines interferon setpoints in healthy humans 216 samples shares microbiome
GSE309135 Dual-transcriptomic analysis of human nasal transcriptome and microbiome reveals host-bacteria interactions associated with symptomatic respiratory infection 202 samples shares microbiome
GSE294364 Antibiotics driven gut microbiome perturbation alters the immune response to the rabies vaccine 176 samples shares microbiome
GSE319236 Spatially resolved maternal and fetal cell contributions to severe Preeclampsia 152 samples shares contributions

Search all human microarray datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.