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EBF1 and PAX5 exert dose dependent epigenetic repression of T-lineage potential [ChIPmentation]

GSE295901 Mus musculus (mouse) Other 16 samples Submitted 2025/11/25 Platform GPL19057
At a glance

mouse · 16 samples

Organism
Mus musculus (mouse)
Samples
16 samples: 8 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.
Paper
B-lineage commitment is dependent on a reversible epigenetic switchGenes & development · 2026
Summary (written by the submitters)
B-lymphocyte development is dependent on the coordinated action of transcription factors controlling the expression of stage and lineage specific genes. To better understand gene regulation and changes in the epigenetic landscape in early B-cell development, we conducted combined SC-RNA/ATAC seq analysis of bone marrow progenitor populations, allowing us to build a developmental trajectory based on changes in epigenetic accessibility.
Read the full summary ↓
This analysis identified a rapid shift in DNA accessibility, where T-lineage primed progenitors gained the epigenetic landscape of B-lymphocytes. The epigenetic switch correlated well with initiation of EBF1 and PAX5 transcription as well as their functional activity. As ectopic expression of EBF1 in Pax5-/- pro-B cells was not sufficient to mediate either the full activation of the B-lineage program of silencing of T-lineage associated genes, we conclude that PAX5 and EBF1 are independently essential for the establishment of the epigenetic landscape in normal B-cell development. This idea was supported by the finding that pro-B cells from mice with combined heterozygote deletion of the Ebf1 and Pax5 genes, carried a non-differentiated epigenetic landscape and expressed T-lineage associated genes. The importance of epigenetic silencing for the preservation of B-cell fate was supported by the finding that inhibition of the histone methylases EZH1 and EZH2 in pro-B cells, allowed for the activation of T-lineage genes and generation of T-lineage cells in response to Notch signaling. Hence, B-lymphoid commitment is associated with a transcription factor dose dependent epigenetic switch, silencing an inherent T-lineage potential in early lymphoid progenitors.
Published in
B-lineage commitment is dependent on a reversible epigenetic switch
Tingvall-Gustafsson J, Hellerstedt K, Ungerbäck J et al. · Genes & development 2026 · PMID 41266087 · doi:10.1101/gad.353002.125
This dataset
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Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗
3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE295901_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA1256762. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41266087) ↗
Study design
8 conditions, mostly in duplicate
WT_BM_proB, H3K4me3, ×2 Ebf1+/-Pax5+/-_BM_proB, H3K4me3, ×2 WT_BM_proB, H3K27ac, ×2 Ebf1+/-Pax5+/-_BM_proB, H3K27ac, ×2 WT_BM_proB, H3K27me3, ×2 Ebf1+/-Pax5+/-_BM_proB, H3K27me3, ×2 WT_BM_proB, Input, ×2 Ebf1+/-Pax5+/-_BM_proB, Input, ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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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