GEO series

PBRM1 directs PBAF to pericentromeres and protects centromere integrity [CUT&RUN]

GSE235294 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 88 samples Submitted 2025/01/05 Platform GPL34284Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 88 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: 88 samples: 24 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.
Paper: PBRM1 directs PBAF to pericentromeres and protects centromere integrityNature communications · 2025

Summary (written by the submitters)

The specialised structure of the centromere is critical for effective chromosome segregation, but its repetitive nature makes it vulnerable to rearrangements. Centromere fragility can drive tumorigenesis, but protective mechanisms preventing fragility are still not fully understood. The PBAF chromatin remodelling complex is frequently misregulated in cancer, but its role in cancer is incompletely characterized.

Read the full summary ↓

Here, we identify PBAF as a protector of centromere and pericentromere structure with profound consequences for genome stability. A conserved feature of isogenic cell lines lacking PBRM1, a subunit of PBAF, is compromised centromere and pericentromere integrity. PBAF is present at these regions, and binding patterns of PBAF and H3K9 methylation change when PBRM1 is absent. PBRM1 loss creates a dependence on the spindle assembly checkpoint, which represents a therapeutic vulnerability. Importantly, we find that even in the absence of any perturbations, PBRM1 loss leads to centromere fragility, thus identifying a new player in centromere protection.

Published in

PBRM1 directs PBAF to pericentromeres and protects centromere integrity

Lane KA, Harrod A, Wu L et al. · Nature communications 2025 · PMID 40011561 · doi:10.1038/s41467-025-57277-9

This dataset

Open GSE235294 in finder → Find more human 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 GSE235294_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 PRJNA985660 and SRA study SRP444965. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40011561) ↗

Study design

24 conditions, mostly in triplicate

WT IgG low salt ×8 WT IgG high salt ×8 PBRM1KO IgG low salt ×6 PBRM1KO IgG high salt ×6 WT SMARCA4 low salt ×3 WT SMARCA4 high salt ×3 WT CENPB low salt ×3 WT CENPB high salt ×3 +16 more

Supports a between-group comparison across 88 samples.

How we read this: 24 replicated groups read from 88 sample titles; they account for 88 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

GSM7498446 WT SMARCA4 low salt rep 1 WT SMARCA4 low salt
GSM7498447 WT SMARCA4 high salt rep 1 WT SMARCA4 high salt
GSM7498448 WT SMARCA4 low salt rep 2 WT SMARCA4 low salt
GSM7498449 WT SMARCA4 high salt rep 2 WT SMARCA4 high salt
GSM7498450 WT SMARCA4 low salt rep 3 WT SMARCA4 low salt
GSM7498451 WT SMARCA4 high salt rep 3 WT SMARCA4 high salt
GSM7498452 WT CENPB low salt rep 1 WT CENPB low salt
GSM7498453 WT CENPB high salt rep 1 WT CENPB high salt
GSM7498454 WT CENPB low salt rep 2 WT CENPB low salt
GSM7498455 WT CENPB high salt rep 2 WT CENPB high salt
GSM7498456 WT CENPB low salt rep 3 WT CENPB low salt
GSM7498457 WT CENPB high salt rep 3 WT CENPB high salt
GSM7498458 WT H3K27me3 low salt rep 1 WT H3K27me3 low salt
GSM7498459 WT H3K27me3 high salt rep 1 WT H3K27me3 high salt
GSM7498460 WT H3K27me3 low salt rep 2 WT H3K27me3 low salt
GSM7498461 WT H3K27me3 high salt rep 2 WT H3K27me3 high salt
GSM7498462 WT H3K27me3 low salt rep 3 WT H3K27me3 low salt
GSM7498463 WT H3K27me3 high salt rep 3 WT H3K27me3 high salt
GSM7498464 WT IgG low salt rep 1 WT IgG low salt
GSM7498465 WT IgG high salt rep 1 WT IgG high salt
GSM7498466 WT IgG low salt rep 2 WT IgG low salt
GSM7498467 WT IgG high salt rep 2 WT IgG high salt
GSM7498468 WT IgG low salt rep 3 WT IgG low salt
GSM7498469 WT IgG high salt rep 3 WT IgG high salt
GSM7498470 PBRM1KO SMARCA4 low salt rep 1 PBRM1KO SMARCA4 low salt
GSM7498471 PBRM1KO SMARCA4 high salt rep 1 PBRM1KO SMARCA4 high sa…
GSM7498472 PBRM1KO SMARCA4 low salt rep 2 PBRM1KO SMARCA4 low salt
GSM7498473 PBRM1KO SMARCA4 high salt rep 2 PBRM1KO SMARCA4 high sa…
GSM7498474 PBRM1KO SMARCA4 low salt rep 3 PBRM1KO SMARCA4 low salt
GSM7498475 PBRM1KO SMARCA4 high salt rep 3 PBRM1KO SMARCA4 high sa…
GSM7498482 PBRM1KO IgG low salt rep 1 PBRM1KO IgG low salt
GSM7498483 PBRM1KO IgG high salt rep 1 PBRM1KO IgG high salt
GSM7498484 PBRM1KO IgG low salt rep 2 PBRM1KO IgG low salt
GSM7498485 PBRM1KO IgG high salt rep 2 PBRM1KO IgG high salt
GSM7498486 PBRM1KO IgG low salt rep 3 PBRM1KO IgG low salt
GSM7498487 PBRM1KO IgG high salt rep 3 PBRM1KO IgG high salt
GSM7498488 SMARCA4KO SMARCA4 low salt rep 1 SMARCA4KO SMARCA4 low s…
GSM7498489 SMARCA4KO SMARCA4 high salt rep 1 SMARCA4KO SMARCA4 high …
GSM7498490 SMARCA4KO SMARCA4 low salt rep 2 SMARCA4KO SMARCA4 low s…
GSM7498491 SMARCA4KO SMARCA4 high salt rep 2 SMARCA4KO SMARCA4 high …

+ 48 more — browse all 88 samples with per-sample file links →

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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.