Laboratory mice engrafted with natural gut microbiota possess a wildling-like phenotype
RNA-seq (gene expression) · mouse · 160 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
- 160 samples: 78 conditions, mostly in duplicateGroups 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
- Laboratory mice engrafted with natural gut microbiota possess a wildling-like phenotypeNature communications · 2025
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 GSE287225_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 PRJNA1211647 and SRA study SRP557878. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 159 samples.
How we read this: 78 replicated groups read from 160 sample titles; they account for 159 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.
- GSM8741632 M1_A_colon_rep2 M1_A_colon
- GSM8741633 M2_A_colon_rep2 M2_A_colon
- GSM8741634 M3_A_colon_rep2 M3_A_colon
- GSM8741635 M4_A_colon_rep2 M4_A_colon
- GSM8741636 M5_A_colon_rep2 M5_A_colon
- GSM8741637 M1_A_colon_rep3 M1_A_colon
- GSM8741638 M2_A_colon_rep3 M2_A_colon
- GSM8741639 M3_A_colon_rep3 M3_A_colon
- GSM8741640 M4_A_colon_rep3 M4_A_colon
- GSM8741641 M5_A_colon_rep3 M5_A_colon
- GSM8741642 M3_B_colon_rep1 M3_B_colon
- GSM8741643 M4_B_colon_rep1 M4_B_colon
- GSM8741644 M1_B_colon_rep2 M1_B_colon
- GSM8741645 M2_B_colon_rep2 M2_B_colon
- GSM8741646 M5_B_colon_rep2 M5_B_colon
- GSM8741647 M1_B_colon_rep3 M1_B_colon
- GSM8741648 M2_B_colon_rep3 M2_B_colon
- GSM8741649 M3_B_colon_rep3 M3_B_colon
- GSM8741650 M4_B_colon_rep3 M4_B_colon
- GSM8741651 M5_B_colon_rep3 M5_B_colon
- GSM8741652 M1_C_colon_rep2 M1_C_colon
- GSM8741653 M2_C_colon_rep2 M2_C_colon
- GSM8741654 M3_C_colon_rep2 M3_C_colon
- GSM8741655 M4_C_colon_rep2 M4_C_colon
- GSM8741656 M5_C_colon_rep2 M5_C_colon
- GSM8741657 M1_C_colon_rep3 M1_C_colon
- GSM8741658 M2_C_colon_rep3 M2_C_colon
- GSM8741659 M3_C_colon_rep3 M3_C_colon
- GSM8741660 M4_C_colon_rep3 M4_C_colon
- GSM8741661 M5_C_colon_rep3 M5_C_colon
- GSM8741662 M1_D_colon_rep1 M1_D_colon
- GSM8741663 M3_D_colon_rep1 M3_D_colon
- GSM8741664 M5_D_colon_rep1 M5_D_colon
- GSM8741665 M1_D_colon_rep2 M1_D_colon
- GSM8741666 M3_D_colon_rep2 M3_D_colon
- GSM8741667 M5_D_colon_rep2 M5_D_colon
- GSM8741668 M1_D_colon_rep3 M1_D_colon
- GSM8741669 M2_D_colon_rep3
- GSM8741670 M3_D_colon_rep3 M3_D_colon
- GSM8741671 M5_D_colon_rep3 M5_D_colon
+ 120 more — browse all 160 samples with per-sample file links →
- GSE284503 Improving “mice with natural microbiota” model through controlled microbial exposure 9 samples shares microbiota, natural
- GSE240797 The microbiota and T cells non-genetically modulate inherited phenotypes transgenerationally 208 samples shares microbiota, phenotype
- GSE260491 Microbiota of infants consuming secretors or non-secretors mothers milk impacts gut and immune system in mice. 83 samples shares microbiota
- GSE269257 A lack of commensal microbiota influences the male reproductive tract intergenerationally in mice 62 samples shares microbiota
- GSE263577 Fecal microbiota transfer from autoimmune dry eye disease model mice to conventional mice induces ocular surface inflammation and stereotypic B cell receptor repertoire development in lacrimal gland 48 samples shares microbiota
- GSE266230 Rapid modulation of gut microbiota composition by hypothalamic circuits in mice. 39 samples shares microbiota
- GSE312171 Fecal microbiota transplantation mitigates cardiac remodeling and functional impairment in mice with chronic colitis 24 samples shares microbiota
- GSE314569 Impacts on the Placenta-Brain Axis in Pregnant Mice Devoid of Gut Microbiota 23 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.