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Serine tRNAs Compete to Regulate the mRNA Translation Of Serine-sensitive Codons

GSE303964 Homo sapiens (human) RNA-seq (gene expression) 48 samples Submitted 2025/11/05 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 48 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
48 samples: 16 conditions, mostly in triplicateGroups 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
Serine tRNAs compete to regulate the mRNA translation of serine-sensitive codonsScience advances · 2025
Summary (written by the submitters)
Differential mRNA translation efficiency (mTE) of codons is important in regulating protein synthesis, cellular states, and can change in response to amino acid (AA) availability. While the mTE of codons is canonically associated with their corresponding transfer RNA (tRNA) isoacceptors, its regulation by AAs in mammalian cells remains unexplored.
Read the full summary ↓
We found that ELAC2, a 3’ tRNA maturation endonuclease, decreases the mTE of UC[U/C] serine (Ser) codons in response to Ser-limitation. Ablation of ELAC2 restored UC[U/C] mTE but reduced the mTE of AG[U/C] Ser codons. Among the tRNASer isoacceptors, tRNASer(GCU) decreased the most in ELAC2-deficient cells. Surprisingly, tRNASer(GCU) delivery restored AG[U/C] mTE and reduced UC[C/U] mTE in ELAC2-deficient cells. Finally, we deciphered the effects of Ser-sensitive codons on mRNA translation and the human proteome. Our study revealed that in response to Ser-limitation, regulation of tRNASer(GCU) levels fine-tune the mTE of UC[C/U] or AG[U/C] Ser-sensitive codons and shapes the proteome.
Published in
Serine tRNAs compete to regulate the mRNA translation of serine-sensitive codons
Costiniti V, Tran WC, Babu NR et al. · Science advances 2025 · PMID 41237252 · doi:10.1126/sciadv.ady4521
This dataset
Open GSE303964 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 GSE303964_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 PRJNA1217441 and SRA study SRP604218. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41237252) ↗
Study design
16 conditions, mostly in triplicate
8902_sgLUC_wSG_RPF ×3 8902_sgLUC_woSG_RPF ×3 8902_sgELAC2_#7_wSG_RPF ×3 8902_sgELAC2_#7_woSG_RPF ×3 8902_sgELAC2_#9_wSG_RPF ×3 8902_sgELAC2_#9_woSG_RPF ×3 8902_sgLUC_wSG_tRNA ×3 8902_sgLUC_woSG_tRNA ×3 +8 more

Supports a between-group comparison across 48 samples.

How we read this: 16 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

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