GEO series

Analysis of Host and Microbiome Responses to Antibiotics Reveals Microbiota-Independent Effects on Gut Immune Response

GSE293029 Mus musculus (mouse) RNA-seq (gene expression) 64 samples Submitted 2026/07/02 Platform GPL21626

At a glance

RNA-seq (gene expression) · mouse · 64 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 64 samples: 16 conditions, mostly with about 4 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Antibiotics are thought to affect host physiology by altering the gut microbiota. But which effects of antibiotics are microbiota-dependent or -independent is not clear. Here, we present a resource encompassing host and microbiota response to antibiotic treatment and computational tools to analyze them. We show how antibiotic administration routes affect host and microbiota responses and how combining antibiotics alters their individual activity.

Read the full summary ↓

We developed CompoRes, a tool to determine whether perturbation affects the host directly or via the microbiota, and discovered microbiota-independent effects of antibiotic treatment. We found that circadian expression of MHC class II in the colon is functional in germ-free mice and is controlled by feeding via glucose. This expression pattern was lost during vancomycin treatment as the antibiotic altered feeding behaviour in a microbiota-independent manner. Together, our study provides tools for analysis of host response to different microbiota compositions which can also identify microbiota-independent effects of perturbations.

This dataset

Open GSE293029 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, 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, or the whole study as GSE293029_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1242377 and SRA study SRP573361. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

16 conditions, mostly with about 4 replicates each

GF PBS ZT17 ×4 GF Vancomycin ZT17 ×4 GF PBS ZT23 ×4 GF Vancomycin ZT23 ×4 GF PBS ZT 5 ×4 GF Vancomycin ZT5 ×4 GF PBS ZT11 ×4 GF Vancomycin ZT11 ×4 +8 more

Supports a between-group comparison across 64 samples.

How we read this: 16 replicated groups read from 64 sample titles; they account for 64 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

GSM8874186 GF PBS ZT17 replicate 1 GF PBS ZT17
GSM8874187 GF PBS ZT17 replicate 2 GF PBS ZT17
GSM8874188 GF PBS ZT17 replicate 3 GF PBS ZT17
GSM8874189 GF PBS ZT17 replicate 4 GF PBS ZT17
GSM8874190 GF Vancomycin ZT17 replicate 1 GF Vancomycin ZT17
GSM8874191 GF Vancomycin ZT17 replicate 2 GF Vancomycin ZT17
GSM8874192 GF Vancomycin ZT17 replicate 3 GF Vancomycin ZT17
GSM8874193 GF Vancomycin ZT17 replicate 4 GF Vancomycin ZT17
GSM8874194 GF PBS ZT23 replicate 1 GF PBS ZT23
GSM8874195 GF PBS ZT23 replicate 2 GF PBS ZT23
GSM8874196 GF PBS ZT23 replicate 3 GF PBS ZT23
GSM8874197 GF PBS ZT23 replicate 4 GF PBS ZT23
GSM8874198 GF Vancomycin ZT23 replicate 1 GF Vancomycin ZT23
GSM8874199 GF Vancomycin ZT23 replicate 2 GF Vancomycin ZT23
GSM8874200 GF Vancomycin ZT23 replicate 3 GF Vancomycin ZT23
GSM8874201 GF Vancomycin ZT23 replicate 4 GF Vancomycin ZT23
GSM8874202 GF PBS ZT 5 replicate 1 GF PBS ZT 5
GSM8874203 GF PBS ZT 5 replicate 2 GF PBS ZT 5
GSM8874204 GF PBS ZT 5 replicate 3 GF PBS ZT 5
GSM8874205 GF PBS ZT 5 replicate 4 GF PBS ZT 5
GSM8874206 GF Vancomycin ZT5 replicate 1 GF Vancomycin ZT5
GSM8874207 GF Vancomycin ZT5 replicate 2 GF Vancomycin ZT5
GSM8874208 GF Vancomycin ZT5 replicate 3 GF Vancomycin ZT5
GSM8874209 GF Vancomycin ZT5 replicate 4 GF Vancomycin ZT5
GSM8874210 GF PBS ZT11 replicate 1 GF PBS ZT11
GSM8874211 GF PBS ZT11 replicate 2 GF PBS ZT11
GSM8874212 GF PBS ZT11 replicate 3 GF PBS ZT11
GSM8874213 GF PBS ZT11 replicate 4 GF PBS ZT11
GSM8874214 GF Vancomycin ZT11 replicate 1 GF Vancomycin ZT11
GSM8874215 GF Vancomycin ZT11 replicate 2 GF Vancomycin ZT11
GSM8874216 GF Vancomycin ZT11 replicate 3 GF Vancomycin ZT11
GSM8874217 GF Vancomycin ZT11 replicate 4 GF Vancomycin ZT11
GSM8874218 SPF PBS ZT17 replicate 1 SPF PBS ZT17
GSM8874219 SPF PBS ZT17 replicate 2 SPF PBS ZT17
GSM8874220 SPF PBS ZT17 replicate 3 SPF PBS ZT17
GSM8874221 SPF PBS ZT17 replicate 4 SPF PBS ZT17
GSM8874222 SPF Vancomycin ZT17 replicate 1 SPF Vancomycin ZT17
GSM8874223 SPF Vancomycin ZT17 replicate 2 SPF Vancomycin ZT17
GSM8874224 SPF Vancomycin ZT17 replicate 3 SPF Vancomycin ZT17
GSM8874225 SPF Vancomycin ZT17 replicate 4 SPF Vancomycin ZT17

+ 24 more — browse all 64 samples with per-sample file links →

Datasets on a similar topic

GSE293180 Analysis of Host and Microbiome Responses to Antibiotics Reveals Microbiota-Independent Effects on Gut Immune Response [multiabx] 97 samples shares microbiota-independent, antibiotics, microbiome, host
GSE293364 Analysis of Host and Microbiome Responses to Antibiotics Reveals Microbiota-Independent Effects on Gut Immune Response. 101 samples shares microbiota-independent, antibiotics, microbiome, host
GSE229963 The intestinal clock controls host’s metabolic response to diet by driving intestinal metabolic functions and the fiber-dependent microbiome 48 samples shares microbiome, host
GSE262290 Metabolic modeling reveals the aging-associated decline of host–microbiome metabolic interactions in mice 156 samples shares microbiome, host
GSE278548 Metabolic modeling reveals the aging-associated decline of host-microbiome metabolic interactions in mice 119 samples shares microbiome, host
GSE270467 Antibiotics damage the colonic mucus barrier in a microbiota-independent manner 50 samples shares microbiota-independent, antibiotics
GSE260592 Antibiotics damage the colonic mucus barrier in a microbiota-independent manner I 28 samples shares microbiota-independent, antibiotics
GSE268945 Dietary fiber inulin enables intestinal microbiome to clear fructose and protect the host 24 samples shares microbiome, host

Search all mouse RNA-seq datasets in GEO →

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