GEO series

BRD4 O-GlcNAcylation attenuates phase separation to regulate transcription

GSE282031 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 38 samples Submitted 2026/07/29 Platform GPL29480Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 38 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: Homo sapiens (human)
Samples: 38 samples: 18 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)

BRD4 undergoes liquid-liquid phase separation (LLPS) at super-enhancers (SEs) to facilitate gene control. However, the regulatory mechanisms and transcriptional consequences of BRD4 condensation remain elusive. Here, we show that the BRD4 C-terminal intrinsically disordered region (IDR) is a primary interacting region for O-GlcNAc transferase (OGT), enabling O-GlcNAc modifications at 12 potential sites.

Read the full summary ↓

O-GlcNAcylation attenuates BRD4 LLPS, leading to small puncta and increased fluidity, which significantly declines occupancy and transcription at SEs. We further demonstrate that loss of O-GlcNAcylation on BRD4 led to elevated gene expression relating to cell cycle and DNA damage, allowing cells less sensitive to DNA damage and promoting faster growth. Therefore, we identify an O-GlcNAc–mediated regulatory mechanism for BRD4 LLPS that governs gene control at SEs, showcasing how O-GlcNAc modifications can influence transcriptional activities at SEs through a phase separation model.

This dataset

Open GSE282031 in finder → Find more human 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 GSE282031_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 PRJNA1186685 and SRA study SRP545492. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

18 conditions, mostly in duplicate

HeLa cells, Total RNA-seq, WT, ×2 HeLa cells, Total RNA-seq, 12A, ×2 HeLa cells, Chr RNA-seq, WT, ×2 HeLa cells, Chr RNA-seq, 12A, ×2 HeLa cells, Nuc RNA-seq, WT, ×2 HeLa cells, Nuc RNA-seq, 12A, ×2 HeLa cells, Cyto RNA-seq, WT, ×2 HeLa cells, Cyto RNA-seq, 12A, ×2 +12 more

Supports a between-group comparison across 36 samples.

How we read this: 18 replicated groups read from 38 sample titles; they account for 36 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

GSM8634642 HeLa cells, Total RNA-seq, WT, rep1 HeLa cells, Total RNA-s…
GSM8634643 HeLa cells, Total RNA-seq, WT, rep2 HeLa cells, Total RNA-s…
GSM8634644 HeLa cells, Total RNA-seq, 12A, rep1 HeLa cells, Total RNA-s…
GSM8634645 HeLa cells, Total RNA-seq, 12A, rep2 HeLa cells, Total RNA-s…
GSM8634646 HeLa cells, Chr RNA-seq, WT, rep1 HeLa cells, Chr RNA-seq…
GSM8634647 HeLa cells, Chr RNA-seq, WT, rep2 HeLa cells, Chr RNA-seq…
GSM8634648 HeLa cells, Chr RNA-seq, 12A, rep1 HeLa cells, Chr RNA-seq…
GSM8634649 HeLa cells, Chr RNA-seq, 12A, rep2 HeLa cells, Chr RNA-seq…
GSM8634650 HeLa cells, Nuc RNA-seq, WT, rep1 HeLa cells, Nuc RNA-seq…
GSM8634651 HeLa cells, Nuc RNA-seq, WT, rep2 HeLa cells, Nuc RNA-seq…
GSM8634652 HeLa cells, Nuc RNA-seq, 12A, rep1 HeLa cells, Nuc RNA-seq…
GSM8634653 HeLa cells, Nuc RNA-seq, 12A, rep2 HeLa cells, Nuc RNA-seq…
GSM8634654 HeLa cells, Cyto RNA-seq, WT, rep1 HeLa cells, Cyto RNA-se…
GSM8634655 HeLa cells, Cyto RNA-seq, WT, rep2 HeLa cells, Cyto RNA-se…
GSM8634656 HeLa cells, Cyto RNA-seq, 12A, rep1 HeLa cells, Cyto RNA-se…
GSM8634657 HeLa cells, Cyto RNA-seq, 12A, rep2 HeLa cells, Cyto RNA-se…
GSM8634658 HeLa cells, Input
GSM8634659 HeLa cells, ChIP WT, rep1 HeLa cells, ChIP WT,
GSM8634660 HeLa cells, ChIP WT, rep2 HeLa cells, ChIP WT,
GSM8634661 HeLa cells, ChIP 12A, rep1 HeLa cells, ChIP 12A,
GSM8634662 HeLa cells, ChIP 12A, rep2 HeLa cells, ChIP 12A,
GSM9038246 HeLa cells, DisP WT, DMSO, rep1 HeLa cells, DisP WT, DM…
GSM9038247 HeLa cells, DisP WT, DMSO, rep2 HeLa cells, DisP WT, DM…
GSM9038248 HeLa cells, DisP WT, bisox, rep1 HeLa cells, DisP WT, bi…
GSM9038249 HeLa cells, DisP WT, bisox, rep2 HeLa cells, DisP WT, bi…
GSM9038250 HeLa cells, DisP 12A, DMSO, rep1 HeLa cells, DisP 12A, D…
GSM9038251 HeLa cells, DisP 12A, DMSO, rep2 HeLa cells, DisP 12A, D…
GSM9038252 HeLa cells, DisP 12A, bisox, rep1 HeLa cells, DisP 12A, b…
GSM9038253 HeLa cells, DisP 12A, bisox, rep2 HeLa cells, DisP 12A, b…
GSM9787149 HeLa cells, ChIP WT, mock, rep1 HeLa cells, ChIP WT, mo…
GSM9787150 HeLa cells, ChIP WT, mock, rep2 HeLa cells, ChIP WT, mo…
GSM9787151 HeLa cells, ChIP WT, siYTHDC1, rep1 HeLa cells, ChIP WT, si…
GSM9787152 HeLa cells, ChIP WT, siYTHDC1, rep2 HeLa cells, ChIP WT, si…
GSM9787153 HeLa cells, ChIP 12A, mock, rep1 HeLa cells, ChIP 12A, m…
GSM9787154 HeLa cells, ChIP 12A, mock, rep2 HeLa cells, ChIP 12A, m…
GSM9787155 HeLa cells, ChIP 12A, siYTHDC1, rep1 HeLa cells, ChIP 12A, s…
GSM9787156 HeLa cells, ChIP 12A, siYTHDC1, rep2 HeLa cells, ChIP 12A, s…
GSM9787157 HeLa cells, Input, for siDC1 batch

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