GEO series

H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [CUTnTAG]

GSE304211 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 128 samples Submitted 2026/05/27 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 128 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: 128 samples: 60 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.

Summary (written by the submitters)

Chromatin compartments reorganize dramatically during cell cycle transitions, shifting from a compartmentalized interphase to a condensed mitotic configuration in which large-scale compartment signals are attenuated. While histone modifications are linked to compartment identity, their contribution to compartment organization remains unclear.

Read the full summary ↓

Using meiotic (mouse spermatogenesis) and mitotic (mouse neuronal progenitor cell, mNPC) models, we mapped histone landscapes alongside compartment dynamics. We found that histone H4 lysine 16 acetylation (H4K16ac) strongly tracked compartment reorganization, remaining enriched in A compartments during compartmentalization but redistributing upon chromatin compaction. In spermatogenesis, H4K16ac loss on the X chromosome coincided with condensation and H3K9me3 spreading. Machine learning highlighted H4K16ac as a stronger predictor of compartment transitions than H3K27ac. Acute degradation of MOF, the principal H4K16ac acetyltransferase, disrupted both the spatial distribution and global abundance of H4K16ac and progressively impaired compartmentalization in mNPCs. These results position H4K16ac as a histone modification selectively coupled to chromatin compartment transitions.

This dataset

Open GSE304211 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 GSE304211_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 PRJNA1299391 and SRA study SRP605474. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

60 conditions, mostly in duplicate

SPD, WT, H4K16ac, ×3 SPG, WT, H3K9me3, ×3 SPC, WT, H3K9me3, ×3 mNPC G0_1, MOF-dTAG, dTAG13 (500 nM, 4h), H4K… ×2 SPG, WT, H3K4me3, ×2 mNPC , MOF-dTAG, dTAG13 (500 nM, 0h), RNAP, ×2 SPD, WT, H3K9me3, ×2 mNPC G0_1, MOF-dTAG, dTAG13 (500 nM, 0h), H4K… ×2 +57 more

Supports a between-group comparison across 123 samples.

How we read this: 60 replicated groups read from 128 sample titles; they account for 123 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

GSM9145098 mNPC G0_1, MOF-dTAG, dTAG13 (500 nM, 4h), H4K16ac, rep2 mNPC G0_1, MOF-dTAG, dT…
GSM9145099 mNPC G0_1, MOF-dTAG, dTAG13 (500 nM, 4h), H4K16ac, rep1 mNPC G0_1, MOF-dTAG, dT…
GSM9145100 SPG, WT, H3K4me3, rep2 SPG, WT, H3K4me3,
GSM9145101 SPG, WT, H3K4me3, rep1 SPG, WT, H3K4me3,
GSM9145102 mNPC , MOF-dTAG, dTAG13 (500 nM, 0h), RNAP, rep1 mNPC , MOF-dTAG, dTAG13…
GSM9145103 mNPC , MOF-dTAG, dTAG13 (500 nM, 0h), RNAP, rep2 mNPC , MOF-dTAG, dTAG13…
GSM9145104 SPD, WT, H3K9me3, rep3 SPD, WT, H3K9me3,
GSM9145105 mNPC G0_1, MOF-dTAG, dTAG13 (500 nM, 0h), H4K16ac, rep1 mNPC G0_1, MOF-dTAG, dT…
GSM9145106 mNPC G0_1, MOF-dTAG, dTAG13 (500 nM, 0h), H4K16ac, rep2 mNPC G0_1, MOF-dTAG, dT…
GSM9145107 mNPC G2_M, MOF-dTAG, dTAG13 (500 nM, 0h), H3K27me3, rep1 mNPC G2_M, MOF-dTAG, dT…
GSM9145108 mNPC G2_M, MOF-dTAG, dTAG13 (500 nM, 0h), H3K27me3, rep2 mNPC G2_M, MOF-dTAG, dT…
GSM9145109 mNPC G0_1, MOF-dTAG, dTAG13 (500 nM, 0h), H3K27ac, rep2 mNPC G0_1, MOF-dTAG, dT…
GSM9145110 mNPC G0_1, MOF-dTAG, dTAG13 (500 nM, 0h), H3K27ac, rep1 mNPC G0_1, MOF-dTAG, dT…
GSM9145111 SPD, WT, H4K16ac, rep1 SPD, WT, H4K16ac,
GSM9145112 SPD, WT, H4K16ac, rep2 SPD, WT, H4K16ac,
GSM9145113 mNPC LS, MOF-dTAG, dTAG13 (500 nM, 0h), H3K27ac, rep2 mNPC LS, MOF-dTAG, dTAG…
GSM9145114 mNPC LS, MOF-dTAG, dTAG13 (500 nM, 0h), H3K27ac, rep1 mNPC LS, MOF-dTAG, dTAG…
GSM9145115 MI, WT, RNAPIIser2, rep2 MI, WT, RNAPIIser2,
GSM9145116 MI, WT, RNAPIIser2, rep1 MI, WT, RNAPIIser2,
GSM9145117 mNPC LS, MOF-dTAG, dTAG13 (500 nM, 0h), H3K9me3, rep2 mNPC LS, MOF-dTAG, dTAG…
GSM9145118 mNPC LS, MOF-dTAG, dTAG13 (500 nM, 0h), H3K9me3, rep1 mNPC LS, MOF-dTAG, dTAG…
GSM9145119 SPG, WT, H3K9me3, rep2 SPG, WT, H3K9me3,
GSM9145120 SPG, WT, H3K9me3, rep1 SPG, WT, H3K9me3,
GSM9145121 mNPC G0_1, MOF-dTAG, dTAG13 (500 nM, 4h), TSA (330 nM, 4h), H4K16ac, rep1 mNPC G0_1, MOF-dTAG, dT…
GSM9145122 mNPC G0_1, MOF-dTAG, dTAG13 (500 nM, 4h), TSA (330 nM, 4h), H4K16ac, rep2 mNPC G0_1, MOF-dTAG, dT…
GSM9145123 mNPC LS, MOF-dTAG, dTAG13 (500 nM, 0h), H4K16ac, rep1 mNPC LS, MOF-dTAG, dTAG…
GSM9145124 mNPC LS, MOF-dTAG, dTAG13 (500 nM, 0h), H4K16ac, rep2 mNPC LS, MOF-dTAG, dTAG…
GSM9145125 SPD, WT, H3K9me3, rep1 SPD, WT, H3K9me3,
GSM9145126 mNPC ES, MOF-dTAG, dTAG13 (500 nM, 0h), H3K9me3, rep1 mNPC ES, MOF-dTAG, dTAG…
GSM9145127 mNPC ES, MOF-dTAG, dTAG13 (500 nM, 0h), H3K9me3, rep2 mNPC ES, MOF-dTAG, dTAG…
GSM9145128 MI, WT, H4K16ac, rep1 MI, WT, H4K16ac,
GSM9145129 MI, WT, H4K16ac, rep2 MI, WT, H4K16ac,
GSM9145130 mNPC G2_M, MOF-dTAG, dTAG13 (500 nM, 4h), TSA (330 nM, 4h), H4K16ac, rep1 mNPC G2_M, MOF-dTAG, dT…
GSM9145131 mNPC G2_M, MOF-dTAG, dTAG13 (500 nM, 4h), TSA (330 nM, 4h), H4K16ac, rep2 mNPC G2_M, MOF-dTAG, dT…
GSM9145132 mNPC ES, MOF-dTAG, dTAG13 (500 nM, 0h), H4K16ac, rep2 mNPC ES, MOF-dTAG, dTAG…
GSM9145133 mNPC ES, MOF-dTAG, dTAG13 (500 nM, 0h), H4K16ac, rep1 mNPC ES, MOF-dTAG, dTAG…
GSM9145134 MII, WT, H4K16ac, rep2 MII, WT, H4K16ac,
GSM9145135 MII, WT, H4K16ac, rep1 MII, WT, H4K16ac,
GSM9145136 SPD, WT, H4K16ac, rep3 SPD, WT, H4K16ac,
GSM9145137 mNPC ES, MOF-dTAG, dTAG13 (500 nM, 0h), H3K27ac, rep1 mNPC ES, MOF-dTAG, dTAG…

+ 88 more — browse all 128 samples with per-sample file links →

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