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Microbiota of infants consuming secretors or non-secretors mothers milk impacts gut and immune system in mice.

GSE260491 Mus musculus (mouse) RNA-seq (gene expression) 83 samples Submitted 2024/03/12 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 83 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
83 samples: 14 conditions, mostly with about 7 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.
Paper
Microbiota from human infants consuming secretors or non-secretors mothers' milk impacts the gut and immune system in micemSystems · 2024
Summary (written by the submitters)
Maternal secretor status is one of the determinants of human milk oligosaccharides (HMOs) composition, which in turn changes the gut microbiota composition of infants. To understand if this change in gut microbiota impacts immune cell composition, intestinal morphology and gene expression, day 21-old germ-free mice were transplanted with fecal microbiota from infants whose mothers were either secretors (SMM) or non-secretors (NSM) or from infants consuming dairy-based formula (MFM).
Read the full summary ↓
For each group, one set of mice was supplemented with HMOs. HMO supplementation did not significantly impact the microbiota diversity however, SMM mice had higher abundance of genus Bacteroides, Bifidobacterium, and Blautia, whereas, in the NSM group, there were higher abundance of Akkermansia, Enterocloster, and Klebsiella. In MFM, gut microbiota was represented mainly by Parabacteroides, Ruminococcaceae_unclassified, and Clostrodium_sensu_stricto. In mesenteric lymph node, Foxp3+ T cells and innate lymphoid cells type 2 (ILC2) were increased in MFM mice supplemented with HMOs while in the spleen, they were increased in SMM+HMOs mice. Similarly, serum immunoglobulin A (IgA) was also elevated in MFM+HMOs group. Distinct global gene expression of the gut was observed in each microbiota group, which was enhanced with HMOs supplementation. Overall, our data shows that distinct infant gut microbiota due to maternal secretor status or consumption of dairy-based formula and HMO supplementation impacts immune cell composition, antibody response and intestinal gene expression in a mouse model.
Published in
Microbiota from human infants consuming secretors or non-secretors mothers' milk impacts the gut and immune system in mice
Gurung M, Schlegel BT, Rajasundaram D et al. · mSystems 2024 · PMID 38530054 · doi:10.1128/msystems.00294-24
This dataset
Open GSE260491 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 GSE260491_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 PRJNA1081879 and SRA study SRP492380. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38530054) ↗
Study design
14 conditions, mostly with about 7 replicates each
SMM, Ileum, ×7 SMM + HMOs, Ileum, ×7 NSM, Ileum, ×7 NSM + HMOs, Ileum, ×7 SMM, Colon, ×7 SMM + HMOs, Colon, ×7 NSM, Colon, ×7 NSM + HMOs, Colon, ×7 +6 more

Supports a between-group comparison across 83 samples.

How we read this: 14 replicated groups read from 83 sample titles; they account for 83 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

+ 43 more — browse all 83 samples with per-sample file links →

Datasets on a similar topic

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