Single-cell transcriptomics of bronchoalveolar lavage reveals divergent macrophage subpopulations and trajectories in interstitial lung disease
Single-cell RNA-seq · human · 9 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
- 9 samples: 4 × BAL_scRNA_Sample vs 3 × RZ734_Pool vs 2 × RZ725_PoolGroups 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.
- Paper
- Single-cell transcriptomics of bronchoalveolar lavage reveals divergent macrophage subpopulations and trajectories in interstitial lung diseasePloS one · 2026
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE296682_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1260524 and SRA study SRP583965. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 9 sample titles; they account for 9 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.
- GSM8974592 BAL_scRNA_Sample3 BAL_scRNA_Sample
- GSM8974593 BAL_scRNA_Sample10 BAL_scRNA_Sample
- GSM8974594 BAL_scRNA_Sample15 BAL_scRNA_Sample
- GSM8974595 BAL_scRNA_Sample18 BAL_scRNA_Sample
- GSM8974596 RZ725_Pool4 RZ725_Pool
- GSM8974597 RZ725_Pool5 RZ725_Pool
- GSM8974598 RZ734_Pool_1 RZ734_Pool
- GSM8974599 RZ734_Pool_2 RZ734_Pool
- GSM8974600 RZ734_Pool_3 RZ734_Pool
- GSE217516 Single-cell RNA-sequencing of bronchoalveolar lavage cells from humans with bronchiectasis 6 samples shares bronchoalveolar, single-cell, lavage
- GSE263448 Multi-omic signatures of sarcoidosis and progression in bronchoalveolar lavage cells 46 samples shares bronchoalveolar, lavage
- GSE287352 Single-cell landscape analysis reveals distinct regression trajectories and novel prognostic biomarkers in primary neuroblastoma 22 samples shares trajectories, single-cell
- GSE264182 Iron-induced oxidative stress alters the transcriptome of bronchoalveolar lavage cells in silicosis 19 samples shares bronchoalveolar, lavage
- GSE252465 Early-stage idiopathic pulmonary fibrosis is characterized by bronchoalveolar accumulation of SPP1+ macrophages 16 samples shares bronchoalveolar, macrophage
- GSE303859 Profibrotic monocyte-derived alveolar macrophages as a biomarker and therapeutic target in systemic sclerosis-associated interstitial lung disease [Northwestern] 15 samples shares interstitial, macrophage
- GSE300946 Bronchoalveolar lavage of healthy human adults after LPS exposure 15 samples shares bronchoalveolar, lavage
- GSE333596 Single-Cell RNA Sequencing Identifies Stem-Like Subpopulations and Their Gene Signature in Lung Adenocarcinoma Progression 12 samples shares subpopulations, single-cell
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.