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Directed evolution improves the catalytic efficiency of APEX2-mediated proximity-dependent RNA labeling

GSE262170 Homo sapiens (human) RNA-seq (gene expression) 54 samples Submitted 2026/03/26 Platform GPL20795
At a glance

RNA-seq (gene expression) · human · 54 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
54 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
Directed Evolution Improves the Catalytic Efficiency of APEX2-Mediated Proximity-Dependent RNA LabelingAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
Summary (written by the submitters)
Engineered ascorbate peroxidase APEX2 has seen widely used for spatially restricted profiling of subcellular biomolecules, but its catalytic efficiency toward newly developed probes such as biotin-aniline (Btn-An) remains suboptimal. To overcome this limitation, we performed yeast surface display based directed evolution to enhance APEX2 activity toward Btn-An.
Read the full summary ↓
The resulting variant, L242FAPEX2, exhibits an approximately two-fold improvement in labeling efficiency, likely through enhanced enzyme-substrate interactions. This increased activity enables rapid and efficient proximity labeling while maintaining spatial specificity. After validating its performance at the ER membrane, we applied L242FAPEX2 to profile the transcriptome proximal to the midbody and identified ANLN as a previously unreported midbody-localized mRNA during telophase. Drug perturbation and reporter assays further revealed that ANLN mRNA targeting to the midbody occurs co-translationally and depends on its nascent N-terminal peptide. Together, this work establishes L242FAPEX2 as an improved and versatile tool for spatially resolved transcriptomics in complex subcellular contexts.
Published in
Directed Evolution Improves the Catalytic Efficiency of APEX2-Mediated Proximity-Dependent RNA Labeling
Wang G, Li Y, Meng P et al. · Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2026 · PMID 41903118 · doi:10.1002/advs.75012
This dataset
Open GSE262170 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 GSE262170_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 PRJNA1090511 and SRA study SRP497026. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41903118) ↗
Study design
16 conditions, mostly in triplicate
BIRC5-APEX2_L242F-EGFP, Btn-An labeling, post… ×4 BIRC5-APEX2_L242F-EGFP, Btn-An labeling, pre-… ×4 BIRC5-APEX2_L242F-EGFP, omit H2O2, post-enric… ×4 KIF23-APEX2_L242F-EGFP, Btn-An labeling, post… ×4 KIF23-APEX2_L242F-EGFP, Btn-An labeling, pre-… ×4 KIF23-APEX2_L242F-EGFP, omit H2O2, post-enric… ×4 APEX2_L242F-NES, Btn-An labeling, post-enrich… ×3 APEX2_L242F-ERM, omit probe, post-enrichment, ×3 +8 more

Supports a between-group comparison across 54 samples.

How we read this: 16 replicated groups read from 54 sample titles; they account for 54 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

+ 14 more — browse all 54 samples with per-sample file links →

Datasets on a similar topic

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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.