GEO series

RNAseq of GMP from mice treated with DSS, HK-EF or its excipient.

GSE281376 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2025/01/22 Platform GPL17021

At a glance

RNA-seq (gene expression) · mouse · 18 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: 18 samples: 6 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: Microbiota translocation following intestinal barrier disruption promotes Mincle-mediated training of myeloid progenitors in the bone marrowImmunity · 2025

Summary (written by the submitters)

Inflammatory bowel disease induced by treatment with DSS induce destruction of gut barrier inducing massive bacterial translocation to distal tissue. Our findings suggest that gut microbiota translocation induces trained immunity in Granulocyte-monocyte progenitors that can underlie pathologies related to low-grade systemic inflammation.

Read the full summary ↓

The identification of E.faecalis translocation to the bone marrow as a main driver of this effect and its sensing by Mincle receptor in bone marrow progenitors offers potential targets for intervention in pathophysiological settings where gut permeability is altered. Moreover, intravenously and intranasal administration of HK-EF provided protection against systemic candidiasis in wild-type and Rag1-deficient mice lacking functional lymphocytes, indicative of innate immune-mediated protection.

Published in

Microbiota translocation following intestinal barrier disruption promotes Mincle-mediated training of myeloid progenitors in the bone marrow

Robles-Vera I, Jarit-Cabanillas A, Brandi P et al. · Immunity 2025 · PMID 39848243 · doi:10.1016/j.immuni.2024.12.012

This dataset

Open GSE281376 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 GSE281376_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 PRJNA1183752. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39848243) ↗

Study design

6 conditions, mostly in triplicate

b_dss ×3 b_hk_ef ×3 bqv ×3 Ct ×3 dss ×3 hk_ef ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM8619479 b_dss_1 b_dss
GSM8619480 b_dss_2 b_dss
GSM8619481 b_dss_3 b_dss
GSM8619482 b_hk_ef_1 b_hk_ef
GSM8619483 b_hk_ef_2 b_hk_ef
GSM8619484 b_hk_ef_3 b_hk_ef
GSM8619485 bqv_1 bqv
GSM8619486 bqv_2 bqv
GSM8619487 bqv_3 bqv
GSM8619488 Ctr1 Ct
GSM8619489 Ctr2 Ct
GSM8619490 Ctr3 Ct
GSM8619491 dss_1 dss
GSM8619492 dss_2 dss
GSM8619493 dss_3 dss
GSM8619494 hk_ef_1 hk_ef
GSM8619495 hk_ef_2 hk_ef
GSM8619496 hk_ef_3 hk_ef

Datasets on a similar topic

GSE281375 Cut&Tag of GMP from mice treated with DSS, HK-EF or its excipient. 18 samples shares hk-ef, gmp, dss, excipient, treated
GSE230337 ATAC-Seq based chromatin accessibilty profile of GMP from mice treated with DSS, HK-EF or its excipient. 18 samples shares hk-ef, gmp, dss, excipient, treated
GSE233491 Bulk TCR-sequencing of various tissues in mice treated with 2% DSS or H2O control. 45 samples shares dss, treated
GSE312324 RNA-sequencing analysis of wild-type, Lao1 knockout and Lao1/Il4i1 double knockout mice under normal and DSS-treated conditions 18 samples shares dss, treated
GSE327232 Transcriptomic profiling of splenic CD4+ T cells in DSS-induced colitis mice treated with Akkermansia muciniphila 6 samples shares dss, treated
GSE278437 Gene expression profile at single cell level of intraepithelial neutrophils (IENs) and lamina propria neutrophils (LPNs) of the colon from dextran sulfate sodium (DSS)-treated mice 4 samples shares dss, treated
GSE310970 Fetal brain RNA-seq of DSS treated or DSS+ Gsdmd-cko 6 samples shares dss, treated
GSE183687 Transcriptomic profiling of isolated hepatic macrophage subsets (Kupffer cells, Monocyte-derived Macrophages and Monocytes) in common bile duct ligated (CBDL)-mice, mice with acute colitis (DSS), and combinations (CBDL+DSS) 58 samples shares dss

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.