Improving “mice with natural microbiota” model through controlled microbial exposure
RNA-seq (gene expression) · mouse · 9 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
- 9 samples: 3 × gav vs 3 × gaf vs 3 × spfGroups 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
- A gavage-fomite based method to generate mouse models with natural microbiotabioRxiv : the preprint server for biology · 2026
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE284503_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1199442 and SRA study SRP552080. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 9 sample titles; they account for 9 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.
- GSM8685586 gav1 gav
- GSM8685587 gav2 gav
- GSM8685588 gav3 gav
- GSM8685589 gaf1 gaf
- GSM8685590 gaf2 gaf
- GSM8685591 gaf3 gaf
- GSM8685592 spf1 spf
- GSM8685593 spf2 spf
- GSM8685594 spf3 spf
- GSE287225 Laboratory mice engrafted with natural gut microbiota possess a wildling-like phenotype 160 samples shares microbiota, natural
- GSE283495 Intestinal epithelial cell diversity and function in respect to age, anatomical localization, and microbial exposure - the global transcriptome 29 samples shares microbial, exposure
- GSE281377 Microbiota exposure following DSS-induced colitis promotes Mincle-mediated training of myeloid progenitors 54 samples shares microbiota, exposure
- GSE319612 Rothia mucilaginosa Alleviates Constipation through Gut Microbiota Remodeling and Neuroactive Pathway Activation 26 samples shares microbiota
- GSE322803 Gut Microbiota Dysbiosis Remodels the Multi-Tissue Transcriptional Landscape of the Host 54 samples shares microbiota
- GSE247323 Maternal indole supplementation protects offspring from NAFLD through altered microbiota- and AHR-mediated ceramide metabolism 40 samples shares microbiota
- GSE342666 Sodium oxybate, a narcolepsy therapeutic, remodels the gut microbiota and alleviates metabolic dysfunction in developing and established obesity 32 samples shares microbiota
- GSE312171 Fecal microbiota transplantation mitigates cardiac remodeling and functional impairment in mice with chronic colitis 24 samples shares microbiota
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.