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The crosstalk between BMP and Wnt signaling establishes the equilibrium of villus length in mammalian small intestine

GSE247044 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/04/28 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples: 3 × WT_proximal vs 3 × WT_distal vs 3 × Bmpr1a_proximal vs 3 × Bmpr1a_distalGroups 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: Positional BMP signaling orchestrates villus length in the small intestineNature communications · 2025

Summary (written by the submitters)

The precise regulatory mechanisms governing the quantitative balance of epithelial cells in the small intestine have long remained elusive. In this study, we reveal a gradual strengthening of BMP signaling from the proximal to distal segments. Through the utilization of genetically engineered mice, we demonstrate that BMP signaling plays a pivotal role in governing villus length.

Read the full summary ↓

Furthermore, employing mathematical modeling, we uncover that BMP signaling acts as a cellular positional information sensor, orchestrating cell apoptosis and inhibiting cell proliferation. This collective regulation of cellular processes leads to the observed disparities in villus length between the proximal and distal segments of the small intestine. Notably, BMP signaling inhibits Wnt signaling to control the rate of villus growth, while Wnt signaling reciprocally upregulates BMP to maintain villus length under conditions of excessive proliferation. The spatial crosstalk between BMP and Wnt signaling networks collectively ensures the homeostasis of villus length. Our comprehensive investigation of the key factors underlying the gradient differences in villus length provides crucial insights for a deeper understanding of the functional dynamics of the small intestine.

Published in

Positional BMP signaling orchestrates villus length in the small intestine

Wang X, Li S, Liu Y et al. · Nature communications 2025 · PMID 40595493 · doi:10.1038/s41467-025-60643-2

This dataset

Open GSE247044 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 GSE247044_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 PRJNA1036121 and SRA study SRP470328. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40595493) ↗

Study design

3 × WT_proximal vs 3 × WT_distal vs 3 × Bmpr1a_proximal vs 3 × Bmpr1a_distal

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM7882548 WT_proximal_1 WT_proximal
GSM7882549 WT_proximal_2 WT_proximal
GSM7882550 WT_proximal_3 WT_proximal
GSM7882551 WT_distal_1 WT_distal
GSM7882552 WT_distal_2 WT_distal
GSM7882553 WT_distal_3 WT_distal
GSM7882554 Bmpr1a_proximal_1 Bmpr1a_proximal
GSM7882555 Bmpr1a_proximal_2 Bmpr1a_proximal
GSM7882556 Bmpr1a_proximal_3 Bmpr1a_proximal
GSM7882557 Bmpr1a_distal_1 Bmpr1a_distal
GSM7882558 Bmpr1a_distal_2 Bmpr1a_distal
GSM7882559 Bmpr1a_distal_3 Bmpr1a_distal

Datasets on a similar topic

GSE313351 Intestinal BMP SMADs impart the mid-villus pattern via direct targeting of villus zonation genes and by controlling a transcription factor hierarchy [RNA-seq] 26 samples shares bmp, villus
GSE339586 Extensive Crosstalk between BMP and Notch Signaling Pathways in Activated Adult Muscle Stem Cells [RNA-seq III] 24 samples shares bmp, crosstalk
GSE244429 BMP9 and BMP10 coordinate liver cellular crosstalk to maintain liver health 24 samples shares bmp, crosstalk
GSE254418 Asymmetric crosstalk between the BMP and TGFβ pathways resolves signaling ambiguity 25 samples shares bmp, crosstalk
GSE305745 Extensive Crosstalk between BMP and Notch Signaling Pathways in Activated Adult Muscle Stem Cells [CUT&Tag] 14 samples shares bmp, crosstalk
GSE313354 Intestinal BMP SMADs impart the mid-villus pattern via direct targeting of villus zonation genes and by controlling a transcription factor hierarchy [CUT&Run] 8 samples shares bmp, villus
GSE267870 Temporal effects of BMP4 on mouse embryonic and extraembryonic development 383 samples shares bmp
GSE247069 Self-organised pattern formation in the developing dorsal neural tube by a temporal relay of BMP signalling 48 samples shares bmp

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