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Intestinal BMP SMADs impart the mid-villus pattern via direct targeting of villus zonation genes and by controlling a transcription factor hierarchy [RNA-seq]

GSE313351 Mus musculus (mouse) RNA-seq (gene expression) 26 samples Submitted 2026/08/05 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 26 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
26 samples: 10 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.
Summary (written by the submitters)
Intestinal villus enterocytes exist in spatially restricted cell states, called zones, and continuously transdifferentiate as they migrate toward the villus tip. Bone morphogenetic protein (BMP) signaling through the BMPR1A receptor is required for zonation of enterocytes; however, the molecular mechanisms and transcriptional regulators downstream of BMP ligands/receptors are unclear.
Read the full summary ↓
Using compound genetic mouse models and epigenomic techniques, we find that SMAD1 and SMAD5 are necessary for activation of middle villus zone genes via direct binding and control of a transcription factor hierarchy. Spatial transcriptomics reveal a homeotic-like shift in the villus pattern of SMAD1/SMAD5 double mutants, with the villus bottom and tip domains expanding at the expense of the middle. Surprisingly, SMAD1 and SMAD5 are not required for regulation of villus tip identity, which is dependent on SMAD4. Epigenomics approaches identify a mechanism for villus patterning in which SMAD1/5 directly activate some mid-villus genes and control others via a transcription factor hierarchy, including a SMAD-regulated transcription factor, TBX3, as a downstream effector of villus zonation.
This dataset
Open GSE313351 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 GSE313351_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 PRJNA1379133 and SRA study SRP654207. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
10 conditions, mostly in triplicate
Proximal SI Epithelium, control (SMAD1/5), 6 … ×3 Proximal SI Epithelium, SMAD1/5 iDKO, 6 days, ×3 Proximal SI Epithelium, control (SMAD1/4/5), … ×3 Proximal SI Epithelium, SMAD1/4/5 iTKO, 30 da… ×3 Proximal SI Epithelium, control (TBX3), 30 da… ×3 Proximal SI Epithelium, iTBX3KO, 30 days, ×3 Proximal SI Epithelium, control (SMAD1/5), 30… ×2 Proximal SI Epithelium, SMAD1/5 iDKO, 30 days, ×2 +2 more

Supports a between-group comparison across 26 samples.

How we read this: 10 replicated groups read from 26 sample titles; they account for 26 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
Datasets on a similar topic

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