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Enzyme-mediated proximity labeling reveals the co-translational targeting of DLGAP5 mRNA to the centrosome during mitosis

GSE260463 Homo sapiens (human) RNA-seq (gene expression) 14 samples Submitted 2025/02/01 Platform GPL20795
At a glance

RNA-seq (gene expression) · human · 14 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
14 samples: 5 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
Enzyme-mediated proximity labeling reveals the co-translational targeting of DLGAP5 mRNA to the centrosome during mitosisRSC chemical biology · 2025
Summary (written by the submitters)
Subcellular RNA localization is a conserved mechanism in eukaryotic cells and plays critical roles in diverse physiological processes including cell proliferation, differentiation, and embryo development. Nevertheless, the characterization of centrosome-localized mRNAs remains under-explored due to technical difficulties. In this study, we utilize APEX2-mediated proximity labeling to map centrosome-proximal transcriptome, identifying DLGAP5 mRNA as a novel centrosome-localized transcript during mitosis.
Read the full summary ↓
Using a combination of drug perturbation, truncation, deletion, and mutagenesis, we demonstrate that microtubule binding of nascent MBD1 polypeptide is required for centrosomal transport of DLGAP5 mRNA. Our data also reveals that mRNA targeting efficiency is tightly linked to the coding sequence length. Thus, our study provides a transcriptomic resource for future investigation of centrosome-localized RNAs, and sheds light on mechanisms underlying mRNA centrosomal localization.
Published in
Enzyme-mediated proximity labeling reveals the co-translational targeting of DLGAP5 mRNA to the centrosome during mitosis
Wang G, Li M, Zou P · RSC chemical biology 2025 · PMID 40248433 · doi:10.1039/d4cb00155a
This dataset
Open GSE260463 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 GSE260463_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 PRJNA1081820 and SRA study SRP492322. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40248433) ↗
Study design
5 conditions, mostly in triplicate
APEX2-NES, BP labeling, post-enrichment, ×3 APEX2-NES, BP labeling, pre-enrichment, ×3 APEX2-PCNT-EGFP, BP labeling, post-enrichment, ×3 APEX2-PCNT-EGFP, BP labeling, pre-enrichment, ×3 APEX2-PCNT-EGFP, omit probe, post-enrichment, ×2

Supports a between-group comparison across 14 samples.

How we read this: 5 replicated groups read from 14 sample titles; they account for 14 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
Datasets on a similar topic

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