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A disrupted compartment boundary underlies abnormal cardiac patterning and congenital heart defects

GSE260601 Mus musculus (mouse) RNA-seq (gene expression) 26 samples Submitted 2025/10/31 Platform GPL24247
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 duplicateGroups 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
A disrupted compartment boundary underlies abnormal cardiac patterning and congenital heart defectsNature cardiovascular research · 2026
Summary (written by the submitters)
Failure of septation of the interventricular septum (IVS) is the most common congenital heart defect (CHD), but mechanisms for patterning the IVS are largely unknown. We show that a Tbx5+/Mef2cAHF+ progenitor lineage forms a compartment boundary bisecting the IVS. This coordinated population originates at a first- and second heart field interface, subsequently forming a morphogenetic nexus.
Read the full summary ↓
Ablation of Tbx5+/Mef2cAHF+ progenitors cause IVS disorganization, right ventricular hypoplasia, and mixing of IVS lineages. Reduced dosage of the CHD transcription factor TBX5 disrupts boundary position and integrity, resulting in ventricular septation defects (VSDs) and patterning defects including Slit2 and Ntn1 misexpression. Reducing NTN1 dosage partly rescues cardiac defects in Tbx5 mutant embryos. Loss of Slit2 or Ntn1 causes VSDs and perturbed septal lineage distributions. Thus, we identify essential cues that direct progenitors to pattern a compartment boundary for proper cardiac septation, revealing new mechanisms for cardiac birth defects.
Published in
A disrupted compartment boundary underlies abnormal cardiac patterning and congenital heart defects
Kathiriya IS, Dominguez MH, Rao KS et al. · Nature cardiovascular research 2026 · PMID 41461901 · doi:10.1038/s44161-025-00755-6
This dataset
Open GSE260601 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 GSE260601_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 PRJNA1082312 and SRA study SRP492631. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41461901) ↗
Study design
10 conditions, mostly in duplicate
control, RV, ×4 control, LV, ×3 mutant, IVS, replicate1, tech ×3 mutant, RV, ×3 control, IVS, replicate1, tech ×2 control, IVS, ×2 control, IVS, replicate4, tech ×2 control, LV, replicate1, tech ×2 +3 more

Supports a case/control comparison: 11 samples read as cases, 15 as controls.

How we read this: 10 replicated groups read from 26 sample titles; they account for 25 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
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