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FXR1 dominates mRNA export fate via riboregulation during hESC differentiation

GSE245777 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2025/08/22 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 36 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
36 samples: 12 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
Modular RNA interactions shape FXR1 condensates involved in mRNA localization and translationNature communications · 2025
Summary (written by the submitters)
mRNA export is required for its translation into functional protein, facilitated by the interaction between mRNA transporters and nuclear pore complex (NPC). However, only a few mRNA transporters associated with NPC were identified. Here, we comprehensively depicted NPC interactome in human embryonic stem cells (hESCs), from which we identified a series of novel mRNA transporters.
Read the full summary ↓
Among them, FXR1 functioned as a cytoplasmic mRNA acceptor, promoted the release of G-quadruplex containing mRNA from its export receptor, simultaneously mediated the localization of nucleoporins mRNA on nuclear pore. FXR1 bound G-quadruplex or nucleoporin AGAA RNA via its RGG and KH domain respectively, which in turn weakened or enhanced its binding to nuclear pore, thus resulted in mRNA release or localization. More importantly, the decline of FXR1 and nuclear pore activity helped hESCs to achieve fate transition by impeding the nuclear export of transcribed RNAs, which was required for hESC differentiation.
Published in
Modular RNA interactions shape FXR1 condensates involved in mRNA localization and translation
Yang J, Chen Z, He J et al. · Nature communications 2025 · PMID 41022782 · doi:10.1038/s41467-025-63700-y
This dataset
Open GSE245777 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 GSE245777_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 PRJNA1029970 and SRA study SRP467339. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41022782) ↗
Study design
12 conditions, mostly in duplicate
hESC(H1) PLKO input ×2 hESC(H1) PLKO Cyto ×2 hESC(H1) PLKO Nuc ×2 hESC(H1) FXR1-KD input ×2 hESC(H1) FXR1-KD Cyto ×2 hESC(H1) FXR1-KD Nuc ×2 hESC(H1) FXR1-OE Cyto. rep1, Day ×2 hESC(H1) FXR1-OE Cyto. rep2, Day ×2 +16 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 36 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
Datasets on a similar topic

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