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Spatial transcriptomics signatures in COPD

GSE293001 synthetic construct; Homo sapiens Spatial transcriptomics 917 samples Submitted 2025/03/28 Platform GPL18573Platform GPL24676Platform GPL19424Platform GPL26526
At a glance

Spatial transcriptomics · synthetic construct; Homo sapiens · 917 samples

What it is
Spatial transcriptomicsGene activity measured with its position in a tissue section.
Organism
synthetic construct; Homo sapiens
Samples
917 samples: 50 conditions, mostly with about 12 replicates eachGroups 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
Lung NR3C1(+) and CXCR6(high) T cells distinguish immunopathogenesis of human emphysemaCommunications biology · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Lung NR3C1(+) and CXCR6(high) T cells distinguish immunopathogenesis of human emphysema
Zhang Y, Sauler M, Corry DB et al. · Communications biology 2025 · PMID 40993192 · doi:10.1038/s42003-025-08698-1
This dataset
Open GSE293001 in finder → Find more 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 GSE293001_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: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.

Also filed as BioProject PRJNA1242323 and SRA study SRP448748. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40993192) ↗
Study design
50 conditions, mostly with about 12 replicates each
DSP-1001660014616-A-A ×13 DSP-1001660014618-B-A ×13 DSP-1001660014616-A-B ×12 DSP-1001660014616-A-C ×12 DSP-1001660014616-A-E ×12 DSP-1001660014616-A-F ×12 DSP-1001660014618-B-B ×12 DSP-1001660011972-E-A ×12 +49 more

Supports a between-group comparison across 393 samples.

How we read this: 50 replicated groups read from the first 400 of 917 sample titles; they account for 393 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

+ 877 more — browse all 917 samples with per-sample file links →

Datasets on a similar topic

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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.