GEO series

Single-cell transcriptomic analysis of GFP-positive and GFP-negative CD45-positive and CD45-negative cardiac cells isolated from TAC-operated REFLEX mice

GSE338857 Mus musculus (mouse) Single-cell RNA-seq 2 samples Submitted 2026/08/03 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 2 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 2 samples
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)

Cardiac remodeling induced by pressure overload is accompanied by extensive changes in intercellular communication among cardiac cell populations. To identify cells that physically interact with vascular endothelial cells in vivo, we utilized the REFLEX system combined with HUNTERuni-seq, a single-cell transcriptomic approach for profiling interacting cell populations.

Read the full summary ↓

Cdh5-CreERT2;REFLEX mice were subjected to transverse aortic constriction (TAC), and GFP-positive cells representing endothelial-interacting cells were isolated from the heart. Single-cell RNA sequencing was performed to characterize the cellular composition and transcriptional states of interacting and non-interacting cell populations in the pressure-overloaded myocardium. These data provide a resource for investigating endothelial-centered cellular interaction networks during cardiac remodeling.

This dataset

Open GSE338857 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 GSE338857_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 PRJNA1496266 and SRA study SRP718534. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 2 more — browse all 2 samples with per-sample file links →

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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.