← BioTransfer GEO Dataset Finder
GEO series

Tolerability and Safety of Nintedanib and Immunosuppression in Autoimmune Inflammatory Myopathy and Progressive Pulmonary Fibrosis

GSE299128 Homo sapiens (human) RNA-seq (gene expression) 57 samples Submitted 2026/08/05 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 57 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
57 samples: 7 conditions, mostly with about 9 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
Tolerability and Safety of Nintedanib and Immunosuppression in Autoimmune Inflammatory Myopathy-Associated Progressive Pulmonary FibrosisCHEST pulmonary · 2026
Summary (written by the submitters)
Introduction: Autoimmune-inflammatory myopathy related interstitial lung disease (AIM-ILD) are often progressive and fibrotic. Given the rarity of this disease, little is known about the safety and tolerability of nintedanib, an anti-fibrotic treatment, in combination with immunosuppression in this population. The objective of this single-arm, open-label trial was to assess safety and tolerability of nintedanib in AIM-ILD, and to determine if peripheral blood cell gene expression changes with administration of nintedanib.
Read the full summary ↓
Methods: Patients with progressive, fibrotic AIM-ILD on background immunosuppression enrolled in this trial were given nintedanib for 24 weeks. Primary endpoint was the percentage of subjects who took 90% or more of the study drug doses. Secondary endpoints included safety (adverse events) and efficacy (lung function) outcomes. Bulk RNA sequencing of peripheral blood was performed at baseline and each subsequent visits to examine gene expression. Results: Eleven participants were enrolled, of which nine completed the study visits as per protocol at 24 weeks. The trial was discontinued due to slow recruitment. Only 3 (27%) participants took 90% or more doses of nintedanib. Drug compliance ranged from 27% to 95%. The most common adverse events were diarrhea, nausea / vomiting, and abdominal pain. There were no significant changes in lung function over time. No difference in gene expression over time was identified. Conclusions: Our trial was limited by small sample size and challenging recruitment, making clear conclusions on safety and tolerability difficult. The nintedanib treatment did not induce measurable gene expression changes in peripheral blood. Based on this small population, tolerability of nintedanib with immunosuppression in AIM-ILD appears challenging.
Published in
Tolerability and Safety of Nintedanib and Immunosuppression in Autoimmune Inflammatory Myopathy-Associated Progressive Pulmonary Fibrosis
Assayag D, Brilland B, Hudson M et al. · CHEST pulmonary 2026 · PMID 42548349 · doi:10.1016/j.chpulm.2025.100230
This dataset
Open GSE299128 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 GSE299128_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 PRJNA1272619 and SRA study SRP590250. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42548349) ↗
Study design
7 conditions, mostly with about 9 replicates each
Whole blood, patient 07, visit # ×9 Whole blood, patient 11, visit # ×9 Whole blood, patient 12, visit # ×9 Whole blood, patient 13, visit # ×9 Whole blood, patient 09, visit # ×8 Whole blood, patient 10, visit # ×8 Whole blood, patient 08, visit # ×5

Supports a between-group comparison across 57 samples.

How we read this: 7 replicated groups read from 57 sample titles; they account for 57 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

+ 17 more — browse all 57 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.