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Post-replicative initial expression of the cell fate regulator PAX6 during neuroectoderm formation [RNA-seq 1]

GSE291903 Homo sapiens (human) RNA-seq (gene expression) 14 samples Submitted 2025/09/22 Platform GPL24676
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: 7 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
Post-replicative initial expression of PAX6 during neuroectoderm differentiationThe EMBO journal · 2025
Summary (written by the submitters)
Human neuroepithelial cells are the earliest neural progenitor cells (NPC) during brain development. The cell cycle is fundamental for cell proliferation and differentiation. How the cell cycle is linked to the differentiation process from embryonic stem cells (ESC) in blastocytes to neuroepithelial cells, however, is still unclear. In this study, using an in vitro ESC-to-NPC differentiation system and PAX6 as an NPC cell fate indicator, we discovered that the neural cell fate was transited, PAX6 expression exhibiting an incremental rise, during the G2 phase.
Read the full summary ↓
For the mechanism, the loss of -401 bp to -450 bp from the transcription start site (TSS) of PAX6 efficiently blocked the cell cycle-dependent expression of PAX6. In addition, we found that using hydroxyurea to arrest the cell cycle of differentiating NPC could prevent NPC differentiation. Overall, this study reported the first scenario to link cell cycle and cell fate transition during early neurogenesis.
Published in
Post-replicative initial expression of PAX6 during neuroectoderm differentiation
Hu S, Kou R, Su Z et al. · The EMBO journal 2025 · PMID 41120788 · doi:10.1038/s44318-025-00605-y
This dataset
Open GSE291903 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 GSE291903_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 PRJNA1235755 and SRA study SRP570292. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41120788) ↗
Study design
7 conditions, mostly in duplicate
H9 embryonic stem cell replication ×2 neural progenitor cell, differentiated 1 day … ×2 neural progenitor cell, differentiated 2 days… ×2 neural progenitor cell, differentiated 3 days… ×2 neural progenitor cell, differentiated 6 days… ×2 neural progenitor cell, differentiated 18 day… ×2 Neuron, differentiated 35 days replication ×2

Supports a between-group comparison across 14 samples.

How we read this: 7 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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