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NGN3 oscillatory expression controls the timing of human pancreatic endocrine differentiation

GSE281587 Homo sapiens (human) Single-cell RNA-seq 24 samples Submitted 2025/03/31 Platform GPL18573
At a glance

Single-cell RNA-seq · human · 24 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
24 samples: 8 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
NGN3 oscillatory expression controls the timing of human pancreatic endocrine differentiationDevelopmental cell · 2025
Summary (written by the submitters)
Understanding protein expression dynamics is crucial for the mechanistic understanding of cell differentiation. We investigate the dynamics and decoding of NGN3, a transcription factor critical for pancreatic endocrine development. A knock-in endogenous reporter shows that NGN3 protein oscillates with a 13-hour periodicity in human iPS-derived endocrine progenitors and is switched off as cells differentiate to β-like and pre-alpha cells.
Read the full summary ↓
Increasing NGN3 protein stability results in one broad peak of expression instead of oscillations, with a larger peak to trough fold-change. This leads to precocious endocrine differentiation and earlier expression of key NGN3 target genes. Single-cell analysis of dynamics, mathematical modelling and experimental validation suggest that NGN3 oscillations are decoded by fold-change detection (FCD) rather than the level of expression via an incoherent feedforward loop motif (IFFL) that explains both normal and precocious differentiation. Our findings suggest that oscillatory NGN3 dynamics control the timing of differentiation, but not fate specification.
Published in
NGN3 oscillatory expression controls the timing of human pancreatic endocrine differentiation
Miller A, Biga V, Rowntree A et al. · Developmental cell 2025 · PMID 40570854 · doi:10.1016/j.devcel.2025.06.004
This dataset
Open GSE281587 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 GSE281587_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1184757 and SRA study SRP544491. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40570854) ↗
Study design
8 conditions, mostly in triplicate
Day 0 biol ×3 Day 3 biol ×3 Day 6 biol ×3 Day 9 biol ×3 Day 12 biol ×3 Day 15 biol ×3 Day 18 biol ×3 Day 24 biol ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 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
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