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CUT&RUN profiling of SOX11 and SMARCA4 in mantle cell lymphoma

GSE302906 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 32 samples Submitted 2026/07/16 Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 32 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)
Topic
Mantle cell lymphomaThis series is part of our curated briefing on it.
Samples
32 samples: 8 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
The SOX11:SMARCA4 complex is a driver of oncogenic transcriptional programs in mantle cell lymphomaBlood cancer journal · 2025
Summary (written by the submitters)
CUT&RUN experiments were performed in mantle cell lymphoma (MCL) cell lines (Z138, Granta-519, and JVM2) under different genetic and treatment conditions. In Z138 cells (wild-type and SOX11 knockout), samples were either untreated or treated with the PROTAC degrader AU-15530 0.5 µM for 24 hours. In JVM2 cells, three conditions were tested: parental JVM2, JVM2TRE-SOX11:HA, and JVM2TRE-SOX11:HA treated with AU-15530 0.5 µM for 24 hours.
Read the full summary ↓
Antibodies against SOX11, SMARCA4, and IgG (as negative control) were used. Peaks were called and visualized using BigWig signal tracks, which are provided as supplementary processed data.
Published in
The SOX11:SMARCA4 complex is a driver of oncogenic transcriptional programs in mantle cell lymphoma
De Bolòs A, Carreras-Caballé M, Sureda-Gómez M et al. · Blood cancer journal 2025 · PMID 40739087 · doi:10.1038/s41408-025-01333-6
This dataset
Open GSE302906 in finder → Find more human ChIP / ATAC / CUT&Tag datasets → Mantle cell lymphoma landscape →
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 GSE302906_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 PRJNA1292801 and SRA study SRP601538. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40739087) ↗
Study design
8 conditions, mostly in triplicate
SMARCA4 in Z138WT ×3 SMARCA4 in Z138WT+ AU-15330 ×3 SMARCA4 in Z138SOX11KO ×3 SOX11 in Z138WT ×3 SOX11 in Z138WT+ AU-15330 ×3 SOX11 in Z138SOX11KO ×3 Negative control IgG rabbit in Z138WT ×2 Negative control IgG rabbit in Z138SOX11KO ×2 +10 more

Supports a between-group comparison across 22 samples.

How we read this: 8 replicated groups read from 32 sample titles; they account for 22 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
More Mantle cell lymphoma datasets

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