GEO series

Kdm6b-mediated epigenetic coordination of temporal precision during motor neuron differentiation [RNA-seq]

GSE305767 Mus musculus (mouse) RNA-seq (gene expression) 21 samples Submitted 2025/09/24 Platform GPL34290

At a glance

RNA-seq (gene expression) · mouse · 21 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: Mus musculus (mouse)
Samples: 21 samples: 7 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.

Summary (written by the submitters)

Histone modifiers are crucial for instructing multiple-stage cellular differentiation, yet the mechanisms underlying their temporal precision remain enigmatic. Here, we demonstrate that the H3K27 demethylase Kdm6b acts as an epigenetic regulator, coordinating stepwise motor neuron (MN) differentiation through sequential partnerships with stage-specific transcription factors (TFs).

Read the full summary ↓

Genome-wide profiling reveals a progressive gain in Kdm6b occupancy, especially at distal regulatory elements, as differentiation proceeds. Kdm6b dynamically shapes chromatin landscapes by coordinating H3K27me3 removal with H3K27ac and H3K4me1 acquisition, thereby enabling timed gene activation from MN specification to maturation. Stage-specific inhibition of Kdm6b compromised the ordered expression of developmental genes. Mechanistically, Kdm6b interacts with temporal TFs over time to ensure precise transcriptional control and MN differentiation. Our work elucidates how a single epigenetic regulator achieves temporal fidelity in driving stepwise MN development, and exemplifies a mechanistic insight into epigenetic regulation in determining developmental timing, with broad implications for understanding neurodevelopment and related diseases.dynamic epigenetic choreography to precisely regulate MN developmental programs from early MN fate specification, intermediate cell differentiation and growth to later maturation. The ordered expression of developmental genes was compromised by stage-specific Kdm6b inhibition. Our work resolves how a single epigenetic regulator achieves temporal precision in driving stepwise MN development, with broad implications for neurodevelopment and diseases.

This dataset

Open GSE305767 in finder → Find more mouse 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 GSE305767_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 PRJNA1307565 and SRA study SRP610094. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

7 conditions, mostly in triplicate

RNA-seq in D4 biol ×3 RNA-seq in D4H8 biol ×3 RNA-seq in D4H8 GSKJ4 biol ×3 RNA-seq in D5 biol ×3 RNA-seq in D5 GSKJ4 biol ×3 RNA-seq in D6 biol ×3 RNA-seq in D6 GSKJ4 biol ×3

Supports a between-group comparison across 21 samples.

How we read this: 7 replicated groups read from 21 sample titles; they account for 21 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

GSM9184482 RNA-seq in D4 biol rep 1 RNA-seq in D4 biol
GSM9184483 RNA-seq in D4 biol rep 2 RNA-seq in D4 biol
GSM9184484 RNA-seq in D4 biol rep 3 RNA-seq in D4 biol
GSM9184485 RNA-seq in D4H8 biol rep 1 RNA-seq in D4H8 biol
GSM9184486 RNA-seq in D4H8 biol rep 2 RNA-seq in D4H8 biol
GSM9184487 RNA-seq in D4H8 biol rep 3 RNA-seq in D4H8 biol
GSM9184488 RNA-seq in D4H8 GSKJ4 biol rep 1 RNA-seq in D4H8 GSKJ4 b…
GSM9184489 RNA-seq in D4H8 GSKJ4 biol rep 2 RNA-seq in D4H8 GSKJ4 b…
GSM9184490 RNA-seq in D4H8 GSKJ4 biol rep 3 RNA-seq in D4H8 GSKJ4 b…
GSM9184491 RNA-seq in D5 biol rep 1 RNA-seq in D5 biol
GSM9184492 RNA-seq in D5 biol rep 2 RNA-seq in D5 biol
GSM9184493 RNA-seq in D5 biol rep 3 RNA-seq in D5 biol
GSM9184494 RNA-seq in D5 GSKJ4 biol rep 1 RNA-seq in D5 GSKJ4 biol
GSM9184495 RNA-seq in D5 GSKJ4 biol rep 2 RNA-seq in D5 GSKJ4 biol
GSM9184496 RNA-seq in D5 GSKJ4 biol rep 3 RNA-seq in D5 GSKJ4 biol
GSM9184497 RNA-seq in D6 biol rep 1 RNA-seq in D6 biol
GSM9184498 RNA-seq in D6 biol rep 2 RNA-seq in D6 biol
GSM9184499 RNA-seq in D6 biol rep 3 RNA-seq in D6 biol
GSM9184500 RNA-seq in D6 GSKJ4 biol rep 1 RNA-seq in D6 GSKJ4 biol
GSM9184501 RNA-seq in D6 GSKJ4 biol rep 2 RNA-seq in D6 GSKJ4 biol
GSM9184502 RNA-seq in D6 GSKJ4 biol rep 3 RNA-seq in D6 GSKJ4 biol

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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.