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Decoding human tRNA modifications and crosstalk by enhanced single-read analysis

GSE305027 Homo sapiens (human) RNA-seq (gene expression) 22 samples Submitted 2026/01/30 Platform GPL34281
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: 10 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
Decoding human tRNA modifications and crosstalk by enhanced single-read analysisGenome biology · 2026
Summary (written by the submitters)
tRNA modifications regulate gene expression and protein synthesis. Human tRNAome contains ~40 chemical modification types distributed on average at 13 sites in cytosolic tRNA and 6 sites in mitochondrial tRNA. tRNA modifications display dynamic patterns dependent on cell type and cell state, underscoring the need for advancing methodologies to assess their variations and crosstalks transcriptome-wide.
Read the full summary ↓
Here, we develop enhanced single-read analysis of tRNA crosstalks (eSLAC), an integrative platform that combines the NGS sequencing method of multiplex small RNA sequencing (MSR-seq), expanded capability to measure pseudouridine (Ψ), 5-formylcytidine (f5C), and N4-acetylcytidine (ac4C), and a single-read analysis pipeline that examines the modification-modification and modification-charging crosstalks. We achieve assessments of over 60% of all human tRNA modification sites and assign Ψ sites to three Ψ writer enzymes. Both Ψ-Ψ and Ψ-charging have strong positive crosstalks. Applying polysome tRNA profiling, we identify differential tRNA isodecoder utilization and tRNA Ψ variations in the E-site versus A and P sites on the polysome. Our approach establishes a foundation for revealing the interconnectedness and the functional complexity of the tRNA modome.
Published in
Decoding human tRNA modifications and crosstalk by enhanced single-read analysis
Assari M, Chew BJ, Bayat Tork MA et al. · Genome biology 2026 · PMID 41721424 · doi:10.1186/s13059-026-04009-x
This dataset
Open GSE305027 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 GSE305027_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 PRJNA1303732 and SRA study SRP607758. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41721424) ↗
Study design
10 conditions, mostly in duplicate
PUS1KO-BStreated ×3 PUS7KO-BStreated ×3 WT-NT ×2 WT-BStreated ×2 WT-PBtreated ×2 TRUB1KO-BStreated ×2 Polysome-NT ×2 Polysome-BStreated ×2 +2 more

Supports a case/control comparison: 12 samples read as cases, 2 as controls.

How we read this: 10 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
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