Foundry120 atlas

← IBD single-cell transcriptomics

single cell RNA-seq of CD45+ cell from DSS induced colitic

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Dataset overview

Participants None
Samples 2
Reuse readiness 6.1/10 evidence-backed score

Beta-Glucan modulates monocyte plasticity and differentiation capacity to mitigate DSS-induced colitis.

Lv Y, Fan Y, Gao Q, Chen Q, Hu Y, Wang L, Shi H, Chen E, et al. · eLife · 2026

Abstract

Trained immunity involves the reprogramming of innate immune cells after an initial exposure, resulting in heightened inflammatory responses to subsequent stimuli and enhanced bactericidal capacity during infection. However, this pro-inflammatory state could also exacerbate chronic conditions like inflammatory bowel disease (IBD), which is characterized by persistent inflammation and microbial imbalance. It remains unclear how trained immunity influences IBD pathogenesis and whether it can be harnessed therapeutically. In our study, pretreatment with β-glucan reprogrammed bone marrow hematopoietic progenitors and peripheral monocytes, inducing a profound shift in monocyte plasticity and significantly reducing the severity of dextran sulfate sodium (DSS)-induced colitis. Adoptive transfer of bone marrow or peripheral monocytes from β-glucan-trained mice into naive mice conferred robust protection against colitis, demonstrating that this protective effect is transferable. Trained mice also displayed improved clearance of intestinal bacterial infections. Single-cell RNA sequencing revealed an expansion of reparative Cx3cr1<sup>+</sup> macrophages derived from Ly6C<sup>hi</sup> monocytes, correlating with accelerated colonic epithelial regeneration. Collectively, these findings reveal how β-glucan-induced trained immunity modulates monocyte differentiation to ameliorate experimental colitis, highlighting the potential of harnessing trained immunity as a therapeutic strategy to recalibrate innate immune responses and restore gut homeostasis in IBD, shedding light for future clinical applications.

doi:10.7554/elife.107339 ↗ PMID 42220316 ↗ PMC13225843 ↗

Study facts

Organism
Mus musculus
Platform
10x Chromium 3′ Reagent Kits v3
Age group
—
Disease groups
—
Anatomical sites
—

Data availability

  • Raw counts
  • Processed matrix

File types MTXTSV

Strengths & limitations for reuse

Strengths

  • Raw reads are advertised
  • Raw counts are advertised
  • Processed matrices are advertised

Limitations

  • Not documented: cell metadata are advertised
  • Not documented: participant counts are documented
Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

FieldValueEvidence
assay.assay_type transcriptomic single cell
"library_source": "transcriptomic single cell"

Section samples, offset —
assay.library_chemistry 10x Cellplex oligos; 10x Chromium 3′ Reagent Kits v3
These cells were barcoded with 10 X Cellplex oligos before being encapsulated using the 10 X Chromium 3′ Reagent Kits v3

Section scRNA-seq, offset —
assay.platform 10x Chromium 3′ Reagent Kits v3
encapsulated using the 10 X Chromium 3′ Reagent Kits v3 according to the manufacturer’s instructions

Section scRNA-seq, offset —
assay.reference_genome mm10
Assembly: mm10

Section samples, offset —
assay.sequencing_type scrna_seq
single cell RNA-seq of CD45+ cell from DSS induced colitic

Section series, offset —

Cohort

FieldValueEvidence
cohort.disease_activity_metadata_available True
Single-cell RNA sequencing analysis of CD45 + cells in the colon on day 7 of colitis after 1 week of BG pretreatment.

Section Results, offset —
cohort.treatment_exposure_documented True from source
GEO sample characteristics document treatment/therapy

Section GEO family SOFT, offset —

Data_Assets

FieldValueEvidence
data_assets.open_access True
Public on Jul 28 2025

Section series, offset —
data_assets.processed_matrix True
Supplementary files format and content: filtered_feature_bc_matrix

Section samples, offset —
data_assets.raw_counts True
Supplementary files format and content: filtered_feature_bc_matrix

Section samples, offset —
data_assets.raw_reads True from source
GSE285859_RAW.tar

Section —, offset —

Processing

FieldValueEvidence
processing.cell_type_annotation_method Unbiased clustering with marker-gene-based cell subset identification
Unbiased clustering analysis identified multiple clusters of intestinal immune cell subsets, including monocytes/macrophages ( Ly6c2 , Ccr2, and Adgre1 ), dendritic (DC) ( Cst3 and H2-Aa ), neutrophils ( S100a8/a9 and Ly6g ), B ( Cd79a Cd79b and Cd19 ), Pre B ( Myl4 and Mme ), CD4 T ( Cd3d and Cd4 ), CD8 T ( Cd3d and Cd8a ), natural killer ( Nkg7 ), ILC2 ( Gata3 and Il4 ), and ILC3 ( Rorc and Il22

Section Results > BG ameliorates colitis via enhanced myeloid cell activation independent of adaptive immunity, offset —
processing.doublet_detection_reported True
Doublet cells were filtered by DoubletFinder v3.

Section Materials and methods > scRNA-seq data processing and analysis, offset —
processing.normalization_method LogNormalize with scale factor 10,000
normalization using normalization.method = ‘LogNormalize,’ scale.factor=10,000 were performed.

Section Materials and methods > scRNA-seq data processing and analysis, offset —
processing.quality_control_reported True
First, quality control was performed to create Seurat object with min features >200 and removal of cells having <200 or >8000 expressed genes or >5% mitochondrial counts.

Section Materials and methods > scRNA-seq data processing and analysis, offset —

Specimens

FieldValueEvidence
specimens.number_of_samples 2
"n_samples": 2

Section geo_record_summary, offset —
specimens.participant_to_sample_mapping_available False inferred
sample from three mice were pooled together and analyzed per condition

Section samples, offset —