GEO series
Native long-read RNA sequencing of human monocytes reveals activation-induced alternative splicing toward functional isoforms
GSE297994
Homo sapiens (human)
RNA-seq (gene expression)
22 samples
Submitted 2026/05/04
Platform GPL24106Platform GPL18573
At a glance
RNA-seq (gene expression) · human · 22 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
- 22 samples: 8 × Monocyte short-read RNA-Seq, Ex vivo, healthy voluntee vs 8 × Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy voluntee vs 3 × Monocyte native long-read RNA-Seq, Ex vivo, healthy voluntee vs 3 × Monocyte native long-read RNA-Seq, 3h LPS in vitro activation, healthy volunteeGroups 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
- Regulation of CLK1 Isoform Expression by Alternative Splicing in Activated Human Monocytes Contributes to Activation-Associated TNF ProductionCells · 2025
Summary (written by the submitters)
Alternative splicing is a key mechanism for expanding transcriptomic and proteomic complexity, yet its role in innate immune activation remains incompletely understood. Here, we applied Oxford Nanopore native RNA sequencing to generate an isoform-level transcriptome of primary human monocytes before and after activation with lipopolysaccharide (LPS).
Read the full summary ↓
We identify over 24,000 expressed isoforms, including thousands of previously unannotated variants. Activation with LPS induced widespread isoform-specific expression changes, leading to extensive isoform switching events, which were validated using matched short-read RNA-Seq. These activation-induced shifts enhanced transcript immune-regulatory functions: activated monocytes preferentially express longer, coding-competent isoforms with complete open reading frames, fewer retained introns, and increased domain complexity. By integrating matched Ribo-seq and proteomic data, we demonstrate that these isoform modulations are associated with enhanced translation of immune effector proteins. Together, our findings position alternative splicing as a dynamic and functional regulator of monocyte activation, emphasizing the need for isoform-level resolution to fully understand immune cell function and inflammation.
Published in
van Haaren MJH, Bodelón A, Sijbers LJPM et al.
· Cells 2025
· PMID 41369414
· doi:10.3390/cells14231925
This dataset
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.
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 GSE297994_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1267092 and SRA study SRP587260. Searching any of these in the dataset finder brings you back here.
Study design
8 × Monocyte short-read RNA-Seq, Ex vivo, healthy voluntee vs 8 × Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy voluntee vs 3 × Monocyte native long-read RNA-Seq, Ex vivo, healthy voluntee vs 3 × Monocyte native long-read RNA-Seq, 3h LPS in vitro activation, healthy voluntee
Supports a between-group comparison across 22 samples.
How we read this: 4 replicated groups read from 22 sample titles; they account for 22 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
- GSM9003806 Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 1 Monocyte short-read RNA…
- GSM9003807 Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 2 Monocyte short-read RNA…
- GSM9003808 Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 3 Monocyte short-read RNA…
- GSM9003809 Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 4 Monocyte short-read RNA…
- GSM9003810 Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 5 Monocyte short-read RNA…
- GSM9003811 Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 6 Monocyte short-read RNA…
- GSM9003812 Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 7 Monocyte short-read RNA…
- GSM9003813 Monocyte short-read RNA-Seq, Ex vivo, healthy volunteer 8 Monocyte short-read RNA…
- GSM9003814 Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 1 Monocyte short-read RNA…
- GSM9003815 Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 2 Monocyte short-read RNA…
- GSM9003816 Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 3 Monocyte short-read RNA…
- GSM9003817 Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 4 Monocyte short-read RNA…
- GSM9003818 Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 5 Monocyte short-read RNA…
- GSM9003819 Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 6 Monocyte short-read RNA…
- GSM9003820 Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 7 Monocyte short-read RNA…
- GSM9003821 Monocyte short-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 8 Monocyte short-read RNA…
- GSM9003822 Monocyte native long-read RNA-Seq, Ex vivo, healthy volunteer 1 Monocyte native long-re…
- GSM9003823 Monocyte native long-read RNA-Seq, Ex vivo, healthy volunteer 2 Monocyte native long-re…
- GSM9003824 Monocyte native long-read RNA-Seq, Ex vivo, healthy volunteer 3 Monocyte native long-re…
- GSM9003825 Monocyte native long-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 1 Monocyte native long-re…
- GSM9003826 Monocyte native long-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 2 Monocyte native long-re…
- GSM9003827 Monocyte native long-read RNA-Seq, 3h LPS in vitro activation, healthy volunteer 3 Monocyte native long-re…
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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.