GEO series

Charting Postnatal Heart Development Using In Vivo Single-Cell Functional Genomic [snRNA-Seq]

GSE290989 Mus musculus (mouse) Single-nucleus RNA-seq 8 samples Submitted 2026/07/22 Platform GPL24247

At a glance

Single-nucleus RNA-seq · mouse · 8 samples

What it is: Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism: Mus musculus (mouse)
Samples: 8 samples: 2 × single-nucleus RNA-seq, postnatal day 0, vs 2 × single-nucleus RNA-seq, postnatal day 7, vs 2 × single-nucleus RNA-seq, postnatal day 14, vs 2 × single-nucleus RNA-seq, postnatal day 21,Groups 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)

The transition at birth, marked by increased circulatory demands and rapid growth, necessitates extensive remodeling of the heart’s structure, function, and metabolism. This transformation requires precise spatial and temporal coordination among diverse cardiac cell types; central to this process is cardiomyocyte maturation, yet the regulatory mechanisms driving these changes remain poorly understood.

Read the full summary ↓

Here, we present a temporal and spatial atlas of postnatal hearts by integrating single-nucleus transcriptomics with image-based spatial transcriptomics, which uncovers the dynamic regulatory networks of cardiomyocyte maturation. To functionally interrogate candidate regulators in vivo, we developed Probe-based Indel-detectable Perturb-seq, a high- throughput platform that uses probe-based chemistry to directly capture sgRNA expression, perturbation status, and transcriptomic profiles at single-nucleus resolution. Applying PIP-seq to postnatal cardiac development identified 21 novel regulators of cardiomyocyte maturation, highlighting critical nodal points in this process. Our study establishes a high-resolution framework for dissecting postnatal heart development, underscoring the integrative and highly ordered roles of microenvironment and intercellular communication in cardiomyocyte maturation. Importantly, PIP-seq enables systematic, high-throughput exploration of gene function and networks underlying complex biological processes in their native in vivo context.

This dataset

Open GSE290989 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 GSE290989_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1231126 and SRA study SRP567699. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

2 × single-nucleus RNA-seq, postnatal day 0, vs 2 × single-nucleus RNA-seq, postnatal day 7, vs 2 × single-nucleus RNA-seq, postnatal day 14, vs 2 × single-nucleus RNA-seq, postnatal day 21,

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 8 sample titles; they account for 8 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

GSM8827071 single-nucleus RNA-seq, postnatal day 0, replicate 1 single-nucleus RNA-seq,…
GSM8827072 single-nucleus RNA-seq, postnatal day 0, replicate 2 single-nucleus RNA-seq,…
GSM8827073 single-nucleus RNA-seq, postnatal day 7, replicate 1 single-nucleus RNA-seq,…
GSM8827074 single-nucleus RNA-seq, postnatal day 7, replicate 2 single-nucleus RNA-seq,…
GSM8827075 single-nucleus RNA-seq, postnatal day 14, replicate 1 single-nucleus RNA-seq,…
GSM8827076 single-nucleus RNA-seq, postnatal day 14, replicate 2 single-nucleus RNA-seq,…
GSM8827077 single-nucleus RNA-seq, postnatal day 21, replicate 1 single-nucleus RNA-seq,…
GSM8827078 single-nucleus RNA-seq, postnatal day 21, replicate 2 single-nucleus RNA-seq,…

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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.