GEO series

Fatty acid oxidation downregulation in alveolar epithelial 2 cells promotes acute lung injury in obesity

GSE264369 Mus musculus (mouse) Single-cell RNA-seq 18 samples Submitted 2025/04/18 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 18 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 18 samples: 5 × HFHO vs 5 × LFHO vs 4 × HFRA vs 4 × LFRAGroups 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)

Obesity is associated with increased risk for acute respiratory distress syndrome (ARDS). High fat diet induced obesity was linked to increased lung injury and bronchoalveolar lavage fluid (BALF) free fatty acids in a hyperoxic model of ARDS. In this study, we show significant transcriptional downregulation of fatty acid oxidation (FAO), the mitochondrial process of breaking down fatty acids, in alveolar epithelial type 2 cells (AEC2) of obese compared to lean mice after hyperoxia.

Read the full summary ↓

AEC2 from obese mice exhibited increased intracellular lipids, more severe mitochondrial bioenergetic failure and reduced ATP production after hyperoxia compared to lean mice. FAO downregulation in AEC2 through a genetic mouse model targeting carnitine palmitoyltransferase 1A (Cpt1aloxp/loxpSftpcCreERT2+/– mice) resulted in further increased BALF fatty acids and lung injury in obese mice. High fat diet was associated with markers of impaired alveolar epithelial regeneration after hyperoxia, which include reduced surfactant AEC2 lineage markers, as well as reduced surfactant related phospholipids in hyperoxic AEC2, and increased BALF surface tension. In a reanalysis of a human molecular single-cell lung atlas of COVID19 ARDS, significant downregulation of the FAO signature in AEC2 compared to controls was observed only in ARDS patients with BMI >30, and not those with BMI <30.

This dataset

Open GSE264369 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 GSE264369_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 PRJNA1102267 and SRA study SRP502773. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

5 × HFHO vs 5 × LFHO vs 4 × HFRA vs 4 × LFRA

Supports a between-group comparison across 18 samples.

How we read this: 4 replicated groups read from 18 sample titles; they account for 18 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

GSM8217115 HFHO16 HFHO
GSM8217116 HFHO17 HFHO
GSM8217117 HFHO18 HFHO
GSM8217118 HFHO19 HFHO
GSM8217119 HFHO20 HFHO
GSM8217120 HFRA16 HFRA
GSM8217121 HFRA17 HFRA
GSM8217122 HFRA18 HFRA
GSM8217123 HFRA19 HFRA
GSM8217124 LFHO16 LFHO
GSM8217125 LFHO17 LFHO
GSM8217126 LFHO18 LFHO
GSM8217127 LFHO19 LFHO
GSM8217128 LFHO20 LFHO
GSM8217129 LFRA16 LFRA
GSM8217130 LFRA17 LFRA
GSM8217131 LFRA18 LFRA
GSM8217132 LFRA19 LFRA

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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.