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Gut microbiota depletion delays peripheral nerve development and impairs neuromuscular junction maturation 

GSE210649 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2024/06/10 Platform GPL19057Platform GPL32159
At a glance

RNA-seq (gene expression) · mouse · 36 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
36 samples: 12 conditions, mostly in triplicateGroups 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.
Paper
Gut microbiota depletion delays somatic peripheral nerve development and impairs neuromuscular junction maturationGut microbes · 2024
Summary (written by the submitters)
Perturbance of gut microbiota (GM) composition has implications in onset and progression of an emerging number of diseases. Here we demonstrate a regulatory impact on proper development of the peripheral nervous system (PNS) and its functional connection to skeletal muscles (SM). We analysed peripheral nerves, dorsal root ganglia (DRG) and SM of neonatal and adult mice that were raised as a) germ free (GF) mice, b) gnotobiotic mice, i.e.
Read the full summary ↓
selectively colonised with 12 known gut bacteria (OMM12), or c) colonised with complex GM (CGM). Stereological and morphometrical analysis mainly revealed that absence of GM impairs the development of median nerves, resulting in smaller diameter hypermyelinated axons. Accordingly, transcriptomic analysis on DRG and sciatic nerves highlighted a panel of differentially expressed developmental and myelination genes. Moreover, GF mice demonstrated histologically atrophic SM, impaired formation of neuromuscular junctions, and deregulated expression of related genes. Our results, for the first time, imply the existence of a “GM-PNS-axis”.
Published in
Gut microbiota depletion delays somatic peripheral nerve development and impairs neuromuscular junction maturation
Cescon M, Gambarotta G, Calabrò S et al. · Gut microbes 2024 · PMID 38845453 · doi:10.1080/19490976.2024.2363015
This dataset
Open GSE210649 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 GSE210649_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 PRJNA866547 and SRA study SRP390179. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38845453) ↗
Study design
12 conditions, mostly in triplicate
adultDRG, CGM_96 ×3 adultDRG, GF_96 ×3 adultDRG, OMM12_96 ×3 adultSN, CGM_96 ×3 adultSN, GF_96 ×3 adultSN, OMM12_96 ×3 neonatalDRG, CGM_96 ×3 neonatalDRG, GF_96 ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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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