GEO series

Single Cell RNA-Sequencing Identifies ferroptotic differences of alveolar macrophages in COPD

GSE227691 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2023/05/24 Platform GPL18573

At a glance

Single-cell RNA-seq · human · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 12 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)

Chronic obstructive pulmonary disease (COPD) is currently the fourth leading cause of morbidity and mortality in the world and is predicted to be the third leading cause of death. It is characterized by chronic airway inflammation, lung destruction and remodeling, resulting in irreversible airflow obstruction. We utilized single cell RNA-sequencing (scRNA-Seq) to identify ferroptotic differences and associated biological processes involved in the pathogenesis of COPD.

Read the full summary ↓

We performed scRNA-Seq on lung tissue obtained from donors with non-COPD and mild-to-moderate COPD to identify disease-related genes within different cell types. We identified two populations of alveolar macrophages (AMs) in the human lung that were dysregulated in COPD patients. We discovered that M2-like AMs modulate susceptibility to ferroptosis by disrupting lipid and iron homeostasis both in vivo and in vitro. The discrepancy in sensitivity to ferroptosis can be determined and regulated by HO-1. In contrast, M1-like AMs showed the ability to attenuate oxidative stress and exert resistance to ferroptosis. In addition, the expression of genes within M2-like AMs is also involved in defects in phagocytosis and lysosome distortion. Present scRNA-seq transcriptomic analysis provides a rich data source to further explore lung health and disease, and the development of therapeutic strategies specifically targeting ferroptosis-sensitive alveolar macrophages might be used to develop therapeutic targets..

This dataset

Open GSE227691 in finder → Find more human 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 GSE227691_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 PRJNA946652 and SRA study SRP428193. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37215140) ↗

Samples in this study

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+ 12 more — browse all 12 samples with per-sample file links →

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