GEO series

Single-nucleus and spatial transcriptomic profiling of human lung tissue in chronic obstructive pulmonary disease (COPD)

GSE313090 Homo sapiens (human) Single-nucleus RNA-seq 153 samples Submitted 2025/12/09 Platform GPL24676Platform GPL33762

At a glance

Single-nucleus RNA-seq · human · 153 samples

What it is: Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism: Homo sapiens (human)
Samples: 153 samples: 149 × Human lung snRNA-seq sample JN10XHT vs 4 × Human lung COPD TMAGroups 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: Aberrant cellular communities underlying disease heterogeneity in chronic obstructive pulmonary diseaseNature genetics · 2026

SuperSeries — this record groups several sub-series.

Summary (written by the submitters)

This SuperSeries is composed of the SubSeries listed below.

Published in

Aberrant cellular communities underlying disease heterogeneity in chronic obstructive pulmonary disease

Zhang Y, Wei H, Nouws J et al. · Nature genetics 2026 · PMID 41578022 · doi:10.1038/s41588-025-02480-z

This dataset

Open GSE313090 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 GSE313090_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 PRJNA1378241. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41578022) ↗

Study design

149 × Human lung snRNA-seq sample JN10XHT vs 4 × Human lung COPD TMA

Supports a between-group comparison across 153 samples.

How we read this: 2 replicated groups read from 153 sample titles; they account for 153 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

GSM9287452 Human lung snRNA-seq sample JN10XHT1 Human lung snRNA-seq sa…
GSM9287453 Human lung snRNA-seq sample JN10XHT2 Human lung snRNA-seq sa…
GSM9287454 Human lung snRNA-seq sample JN10XHT3 Human lung snRNA-seq sa…
GSM9287455 Human lung snRNA-seq sample JN10XHT4 Human lung snRNA-seq sa…
GSM9287456 Human lung snRNA-seq sample JN10XHT5 Human lung snRNA-seq sa…
GSM9287457 Human lung snRNA-seq sample JN10XHT6 Human lung snRNA-seq sa…
GSM9287458 Human lung snRNA-seq sample JN10XHT7 Human lung snRNA-seq sa…
GSM9287459 Human lung snRNA-seq sample JN10XHT9 Human lung snRNA-seq sa…
GSM9287460 Human lung snRNA-seq sample JN10XHT10 Human lung snRNA-seq sa…
GSM9287461 Human lung snRNA-seq sample JN10XHT11 Human lung snRNA-seq sa…
GSM9287462 Human lung snRNA-seq sample JN10XHT13 Human lung snRNA-seq sa…
GSM9287463 Human lung snRNA-seq sample JN10XHT14 Human lung snRNA-seq sa…
GSM9287464 Human lung snRNA-seq sample JN10XHT16 Human lung snRNA-seq sa…
GSM9287465 Human lung snRNA-seq sample JN10XHT17 Human lung snRNA-seq sa…
GSM9287466 Human lung snRNA-seq sample JN10XHT18 Human lung snRNA-seq sa…
GSM9287467 Human lung snRNA-seq sample JN10XHT19 Human lung snRNA-seq sa…
GSM9287468 Human lung snRNA-seq sample JN10XHT20 Human lung snRNA-seq sa…
GSM9287469 Human lung snRNA-seq sample JN10XHT21 Human lung snRNA-seq sa…
GSM9287470 Human lung snRNA-seq sample JN10XHT22 Human lung snRNA-seq sa…
GSM9287471 Human lung snRNA-seq sample JN10XHT23 Human lung snRNA-seq sa…
GSM9287472 Human lung snRNA-seq sample JN10XHT26 Human lung snRNA-seq sa…
GSM9287473 Human lung snRNA-seq sample JN10XHT27 Human lung snRNA-seq sa…
GSM9287474 Human lung snRNA-seq sample JN10XHT28 Human lung snRNA-seq sa…
GSM9287475 Human lung snRNA-seq sample JN10XHT29 Human lung snRNA-seq sa…
GSM9287476 Human lung snRNA-seq sample JN10XHT30 Human lung snRNA-seq sa…
GSM9287477 Human lung snRNA-seq sample JN10XHT31 Human lung snRNA-seq sa…
GSM9287478 Human lung snRNA-seq sample JN10XHT32 Human lung snRNA-seq sa…
GSM9287479 Human lung snRNA-seq sample JN10XHT33 Human lung snRNA-seq sa…
GSM9287480 Human lung snRNA-seq sample JN10XHT34 Human lung snRNA-seq sa…
GSM9287481 Human lung snRNA-seq sample JN10XHT35 Human lung snRNA-seq sa…
GSM9287482 Human lung snRNA-seq sample JN10XHT36 Human lung snRNA-seq sa…
GSM9287483 Human lung snRNA-seq sample JN10XHT37 Human lung snRNA-seq sa…
GSM9287484 Human lung snRNA-seq sample JN10XHT38 Human lung snRNA-seq sa…
GSM9287485 Human lung snRNA-seq sample JN10XHT39 Human lung snRNA-seq sa…
GSM9287486 Human lung snRNA-seq sample JN10XHT40 Human lung snRNA-seq sa…
GSM9287487 Human lung snRNA-seq sample JN10XHT41 Human lung snRNA-seq sa…
GSM9287488 Human lung snRNA-seq sample JN10XHT43 Human lung snRNA-seq sa…
GSM9287489 Human lung snRNA-seq sample JN10XHT44 Human lung snRNA-seq sa…
GSM9287490 Human lung snRNA-seq sample JN10XHT45 Human lung snRNA-seq sa…
GSM9287491 Human lung snRNA-seq sample JN10XHT46 Human lung snRNA-seq sa…

+ 113 more — browse all 153 samples with per-sample file links →

Datasets on a similar topic

GSE310058 Single-nucleus transcriptomic profiling of human lung tissue in chronic obstructive pulmonary disease (COPD) [snRNA-seq] 149 samples shares copd, single-nucleus, obstructive, pulmonary, chronic, lung
GSE239897 Mucosal immune alterations at the early onset of tissue destruction in Chronic Obstructive Pulmonary Disease 82 samples shares obstructive, pulmonary, chronic
GSE199345 Siglec-1−/FSClow alveolar macrophages exhibit pro-inflammatory phenotypes in chronic obstructive pulmonary disease 24 samples shares obstructive, pulmonary, chronic
GSE249584 Single cell transcriptomics in blood of patients with chronic obstructive pulmonary disease 15 samples shares obstructive, pulmonary, chronic
GSE268499 Construction of a ceRNA network and screening of potential biomarkers and molecular targets in male smokers with chronic obstructive pulmonary disease 10 samples shares obstructive, pulmonary, chronic
GSE150910 RNA-Sequencing of Chronic hypersensitivity pneumonitis compared with Idiopathic Pulmonary Fibrosis and Control Lung 288 samples shares pulmonary, chronic, lung
GSE194070 Tumor-intrinsic CD74 expression mediates immune evasion in lung cancer with COPD 16 samples shares copd, lung
GSE296912 scRNA-seq of normal and COPD lungs 7 samples shares copd, lung

Search all human RNA-seq datasets in GEO →

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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.