GEO series

Transcriptome profiling of induced sputum identified up-regulated TNF-α/NF-κB signaling and down-regulated mitochondrial respiratory chain function in post-infectious Bronchiolitis obliterans

GSE327957 Homo sapiens (human) RNA-seq (gene expression) 17 samples Submitted 2026/06/03 Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 17 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 17 samples: 9 × sputum_patient_F vs 5 × sputum_control vs 3 × sputum_control_FGroups 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: Transcriptome Profiling of Induced Sputum Identified Upregulated TNF-α/NF-κB Signalling and Downregulated Mitochondrial Respiratory Chain Function in Post-Infectious Bronchiolitis ObliteransBiomolecules · 2026

Summary (written by the submitters)

Post-infectious bronchiolitis obliterans (PiBO) is a chronic lung disease that occurs after severe lower respiratory infections and leads to persistent inflammation and fibrotic changes in the small airways. In the present study, gene expression analysis was used to identify differentially expressed genes (DEGs) in sputum cells derived from PiBO patients compared to healthy controls.

Read the full summary ↓

Clinical history, lung function parameters, and induced sputum samples were collected from nine patients with PiBO and eight healthy controls. Multiplex immunohistochemistry (mIHC) as well as mRNA sequencing (MACE-Seq) were performed. Evaluation of the biological targets was done by KEGG pathway enrichment analysis. PiBO patients showed significantly reduced lung function parameters, an increased neutrophil count, and an altered macrophage profile in sputum. Transcriptome analysis revealed significant upregulation of the TNFα-dependent NFκB signalling pathway, as well as significant downregulation of the oxidative phosphorylation (OXPHOS). Linear regression analyses and mIHC showed a shift in macrophage polarization that appears to be responsible for the dysregulated gene expression. Notably, expression of these DEGs significantly correlated with FEV₁ lung function. These findings indicate a central role of macrophages in the immunopathology of PiBO and contribute to our understanding of the molecular mechanism involved in the disease process.

Published in

Transcriptome Profiling of Induced Sputum Identified Upregulated TNF-α/NF-κB Signalling and Downregulated Mitochondrial Respiratory Chain Function in Post-Infectious Bronchiolitis Obliterans

Jerkic SP, Naegele K, Gronau L et al. · Biomolecules 2026 · PMID 42194095 · doi:10.3390/biom16050745

This dataset

Open GSE327957 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 GSE327957_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1453396 and SRA study SRP691707. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42194095) ↗

Study design

9 × sputum_patient_F vs 5 × sputum_control vs 3 × sputum_control_F

Supports a case/control comparison: 9 samples read as cases, 8 as controls.

How we read this: 3 replicated groups read from 17 sample titles; they account for 17 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

GSM9669373 sputum_patient_F054 sputum_patient_F
GSM9669374 sputum_control_F500 sputum_control_F
GSM9669375 sputum_control_F507 sputum_control_F
GSM9669376 sputum_control_F509 sputum_control_F
GSM9669377 sputum_patient_F002 sputum_patient_F
GSM9669378 sputum_patient_F006 sputum_patient_F
GSM9669379 sputum_patient_F009 sputum_patient_F
GSM9669380 sputum_patient_F017 sputum_patient_F
GSM9669381 sputum_patient_F025 sputum_patient_F
GSM9669382 sputum_patient_F030 sputum_patient_F
GSM9669383 sputum_patient_F034 sputum_patient_F
GSM9669384 sputum_patient_F043 sputum_patient_F
GSM9669385 sputum_control_602 sputum_control
GSM9669386 sputum_control_603 sputum_control
GSM9669387 sputum_control_606 sputum_control
GSM9669388 sputum_control_607 sputum_control
GSM9669389 sputum_control_608 sputum_control

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