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Loss of KAT6B causes premature ossification and promotes osteoblast differentiation during development

GSE287245 Mus musculus (mouse) RNA-seq (gene expression) 32 samples Submitted 2025/11/26 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 32 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
32 samples: 8 conditions, mostly with about 4 replicates eachGroups 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
Loss of KAT6B causes premature ossification and promotes osteoblast differentiation during developmentDevelopmental biology · 2025
Summary (written by the submitters)
The MYST family histone acetyltransferase gene, KAT6B (MYST4, MORF, QKF) is mutated in two distinct human congenital disorders characterised by intellectual disability, facial dysmorphogenesis and skeletal abnormalities, Say-Barber-Biesecker-Young-Simpson variant of Ohdo syndrome and Genitopatellar syndrome. Despite its requirement in normal skeletal development, the cellular and transcription effects of KAT6B in skeletogenesis have not been thoroughly studied.
Read the full summary ↓
In this dataset, we examined the effects of loss of KAT6B on gene expression in proliferating primary mouse embryonic fibroblasts (MEFs) and MEFs induced to differentiated towards chondrocytes, osteoblasts and adipocytes. We show that loss of KAT6B in mesenchymal progenitor cells promotes transition towards an osteoblast-progenitor state with upregulation of gene targets of RUNX2, a master regulators of osteoblast development and concomitant downregulation of SOX9, a critical gene in chondrocyte development.
Published in
Loss of KAT6B causes premature ossification and promotes osteoblast differentiation during development
Bergamasco MI, Ogier JM, Garnham AL et al. · Developmental biology 2025 · PMID 39832706 · doi:10.1016/j.ydbio.2025.01.012
This dataset
Open GSE287245 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 GSE287245_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 PRJNA1211681 and SRA study SRP557912. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39832706) ↗
Study design
8 conditions, mostly with about 4 replicates each
WT proliferating, ×4 Kat6b KO proliferating, ×4 WT pre-adipocyte fat, ×4 Kat6b KO pre-adipocyte fat, ×4 WT pre-chondrocyte cartilage, ×4 Kat6b KO pre-chondrocyte cartilage, ×4 WT pre-osteoblast bone, ×4 Kat6b KO pre-osteoblast bone, ×4

Supports a between-group comparison across 32 samples.

How we read this: 8 replicated groups read from 32 sample titles; they account for 32 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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