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A single-cell atlas of normal and KRASG12D-malformed lymphatic vessels

GSE272843 Mus musculus (mouse) Single-cell RNA-seq 2 samples Submitted 2025/01/23 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.
Paper: A single-cell atlas of normal and KRASG12D-malformed lymphatic vesselsJCI insight · 2025

Summary (written by the submitters)

Somatic activating mutations in KRAS can cause complex lymphatic anomalies (CLAs). However, the specific cellular and molecular processes that drive KRAS-mediated CLAs have yet to be fully elucidated. Here, we use single-cell RNA sequencing to construct an atlas of normal and KrasG12D-malformed lymphatic vessels. We show that adult wild-type mice have six subtypes of lymphatic endothelial cells (LECs) in their lungs (Ptx3, capillary, collecting, valve, mixed, and proliferating).

Read the full summary ↓

To determine when the LEC subtypes are specified during development, we integrated our data with data from four stages of development. We show that proliferating and Ptx3 LECs are prevalent during early lymphatic development and that collecting and valve LECs emerge later in development. Additionally, we demonstrate that the proportion of Ptx3 LECs decreases as the lymphatic network matures but remains high in KrasG12D mice. We also show that KrasG12D mice have fewer collecting and valve LECs than wild-type mice. Last, we demonstrate that immature lymphatic vessels in young mice are more sensitive to the pathologic effects of KrasG12D than mature lymphatic vessels in older mice. Together, our results expand the current model for the development of the lymphatic system and suggest that KRAS mutations impair the maturation of lymphatic vessels.

Published in

A single-cell atlas of normal and KRASG12D-malformed lymphatic vessels

Fernandes LM, Griswold-Wheeler D, Tresemer JD et al. · JCI insight 2025 · PMID 39874106 · doi:10.1172/jci.insight.185181

This dataset

Open GSE272843 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 GSE272843_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 PRJNA1139099 and SRA study SRP521565. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39874106) ↗

Samples in this study

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

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