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Sequence determinants of intron-mediated enhancement learned from thousands of random introns

GSE278584 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2024/10/28 Platform GPL16791Platform GPL34295
At a glance

RNA-seq (gene expression) · human · 24 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
24 samples: 8 conditions, mostly in duplicateGroups 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
Sequence-dependent and -independent effects of intron-mediated enhancement learned from thousands of random intronsNucleic acids research · 2025
Summary (written by the submitters)
Spliceosomal introns are a ubiquitous feature of eukaryotic genes, whose presence often boosts the expression of their host gene, a phenomenon known as intron-mediated enhancement (IME). IME has been noted across diverse genes and organisms, but remains mysterious in many respects. For example, how does intron sequence affect the magnitude of IME?
Read the full summary ↓
In this study, we performed a massively parallel reporter assay (MPRA) to assess the effect of varying intron sequence on gene expression in a high-throughput manner, using tens of thousands of synthetic introns with natural splice sites and randomized internal sequence. We observe that most random introns splice efficiently and enhance gene expression as well as or better than fully natural introns. Nearly all introns stimulate gene expression ~eight-fold above an intronless control, at both mRNA and protein levels, suggesting that the primary mechanism acts to increase mRNA levels. IME strength is positively associated with splicing efficiency and with the intronic content of poly-uridine stretches, which we confirm using reporter experiments. In sum, this work elucidates sequence determinants of IME from tens of thousands of random introns.
Published in
Sequence-dependent and -independent effects of intron-mediated enhancement learned from thousands of random introns
Kowal EJK, Sakai Y, McGurk MP et al. · Nucleic acids research 2025 · PMID 39995040 · doi:10.1093/nar/gkaf097
This dataset
Open GSE278584 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 GSE278584_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 PRJNA1168030 and SRA study SRP536171. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39995040) ↗
Study design
8 conditions, mostly in duplicate
Random intron library, bulk RNA, ×10 Random intron library, iterative FACS RNA, fi… ×2 Random intron library, iterative FACS RNA, se… ×2 Random intron library, iterative FACS RNA, th… ×2 Random intron library, iterative FACS RNA, fi… ×2 Random intron library, iterative FACS RNA, se… ×2 Random intron library, iterative FACS RNA, th… ×2 PolyU library, bulk RNA, ×2

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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
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