GEO series

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

GSE305831 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 26 samples Submitted 2025/09/24 Platform GPL34290

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 26 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 26 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.

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.

This dataset

Open GSE305831 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE305831_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1307991 and SRA study SRP610090. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

5 conditions, mostly in triplicate

Cut&Run-seq Kdm6b in D ×3 Cut&Tag-seq H3K27me3 in D ×3 Cut&Tag-seq H3K27ac in D ×3 Cut&Tag-seq H3K4me1 in D ×3 Cut&Tag-seq H3K4me3 in D ×3 Cut&Run-seq Kdm6b in D4H ×1 Cut&Run-seq Neurod1 in D ×1 Cut&Run-seq Cux1/2 in D ×1 +8 more

Supports a between-group comparison across 15 samples.

How we read this: 5 replicated groups read from 26 sample titles; they account for 15 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

GSM9185895 Cut&Run-seq Kdm6b in D4 Cut&Run-seq Kdm6b in D
GSM9185896 Cut&Run-seq Kdm6b in D4H8
GSM9185897 Cut&Run-seq Kdm6b in D5 Cut&Run-seq Kdm6b in D
GSM9185898 Cut&Run-seq Kdm6b in D6 Cut&Run-seq Kdm6b in D
GSM9185899 Cut&Run-seq Neurod1 in D5
GSM9185900 Cut&Run-seq Cux1/2 in D6
GSM9185901 Cut&Tag-seq H3K27me3 in D4 Cut&Tag-seq H3K27me3 in…
GSM9185902 Cut&Tag-seq H3K27me3 in D4H8
GSM9185903 Cut&Tag-seq H3K27me3 in D5 Cut&Tag-seq H3K27me3 in…
GSM9185904 Cut&Tag-seq H3K27me3 in D6 Cut&Tag-seq H3K27me3 in…
GSM9185905 Cut&Tag-seq H3K27ac in D4 Cut&Tag-seq H3K27ac in D
GSM9185906 Cut&Tag-seq H3K27ac in D4H8
GSM9185907 Cut&Tag-seq H3K27ac in D5 Cut&Tag-seq H3K27ac in D
GSM9185908 Cut&Tag-seq H3K27ac in D6 Cut&Tag-seq H3K27ac in D
GSM9185909 Cut&Tag-seq H3K4me1 in D4 Cut&Tag-seq H3K4me1 in D
GSM9185910 Cut&Tag-seq H3K4me1 in D4H8
GSM9185911 Cut&Tag-seq H3K4me1 in D5 Cut&Tag-seq H3K4me1 in D
GSM9185912 Cut&Tag-seq H3K4me1 in D6 Cut&Tag-seq H3K4me1 in D
GSM9185913 Cut&Tag-seq H3K4me3 in D4 Cut&Tag-seq H3K4me3 in D
GSM9185914 Cut&Tag-seq H3K4me3 in D4H8
GSM9185915 Cut&Tag-seq H3K4me3 in D5 Cut&Tag-seq H3K4me3 in D
GSM9185916 Cut&Tag-seq H3K4me3 in D6 Cut&Tag-seq H3K4me3 in D
GSM9615228 Cut&Run-seq Kdm6b in D4H8 with Olig2-KD
GSM9615229 Cut&Tag-seq H3K27me3 in D5 with GSKJ4
GSM9615230 Cut&Tag-seq H3K27ac in D5 with GSKJ4
GSM9615231 Cut&Tag-seq H3K4me1 in D5 with GSKJ4

Datasets on a similar topic

GSE305767 Kdm6b-mediated epigenetic coordination of temporal precision during motor neuron differentiation [RNA-seq] 21 samples shares kdm6b-mediated, coordination, epigenetic, precision, temporal, neuron
GSE289108 Neurons undergo IFNγ-driven persistent epigenetic shifts and synaptic remodeling in the inflamed brain [ChIP-Seq] 57 samples shares epigenetic, neuron
GSE275917 Nup153 regulates neuronal responsiveness through HDAC1-mediated epigenetic modulation [ChIP-seq] 17 samples shares epigenetic, neuron
GSE243943 Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing 127 samples shares epigenetic, temporal
GSE243942 Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [RNA-seq] 125 samples shares epigenetic, temporal
GSE244496 Establishment of nuclear organization in mouse embryos is regulated by multiple and redundant epigenetic pathways. 183 samples shares epigenetic
GSE289642 Noncanonical PRC2 chromatin association reveals a key role of EZHIP in intergenerational epigenetic memory transition [ChIP-Seq, Cut & Run] 107 samples shares epigenetic
GSE235109 Ensembles of genome-coverage single-cell histone modifications reveal epigenetic lineages during mouse preimplantation development 47 samples shares epigenetic

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

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.