GEO series

Motif-directed chromatin repression by BCL11B shapes ectopic targeting and lineage commitment [ATAC-seq]

GSE327360 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 20 samples Submitted 2026/04/09 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 20 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: 20 samples: 20 samples, each with a distinct title — no replicated groupsGroups 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)

BCL11B encodes a critical T-lineage transcription factor that is implicated as both an oncogene and a tumor suppressor in acute leukemia. Despite its central role in development and malignancy, a basic understanding of the sequence determinants of BCL11B activity remains obscure. Here, we define two functionally distinct modes of BCL11B engagement with chromatin: Most detectable BCL11B binding events are determined by pre-existing patterns of chromatin accessibility and RUNX1 occupancy.

Read the full summary ↓

In contrast, BCL11B directs chromatin closing at genomic regions enriched for DNA motifs containing the core “TGACC” sequence, which are most prevalent in non-T lineages. These BCL11B-closed target sites cannot be identified from conventional BCL11B chromatin profiling approaches yet represent the primary mechanism by which BCL11B regulates gene expression. We provide evidence that cell of origin impacts the ability of BCL11B to repress lineage-inappropriate gene programs, thereby promoting lineage skewing. Together, these findings define a motif-centered determinant of BCL11B repression and explain how BCL11B controls lineage specification.

This dataset

Open GSE327360 in finder → Find more human 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 GSE327360_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 PRJNA1450595 and SRA study SRP690171. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

20 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 20 sample titles: 20 distinct titles with little repetition. 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

GSM9624228 CD34, empty vector, rep1, ATAC
GSM9624229 CD34, empty vector, rep2, ATAC
GSM9624230 CD34, BCL11B, rep1, ATAC
GSM9624231 CD34, BCL11B, rep2, ATAC
GSM9624232 CD34, empty vector, DMSO, rep1, ATAC
GSM9624233 CD34, empty vector, DMSO, rep2, ATAC
GSM9624234 CD34, empty vector, dTAGV-1, rep1, ATAC
GSM9624235 CD34, empty vector, dTAGV-1, rep2, ATAC
GSM9624236 CD34, BCL11B-dTAG, DMSO, rep1, ATAC
GSM9624237 CD34, BCL11B-dTAG, DMSO, rep2, ATAC
GSM9624238 CD34, BCL11B-dTAG, dTAGV-1, rep1, ATAC
GSM9624239 CD34, BCL11B-dTAG, dTAGV-1, rep2, ATAC
GSM9624240 Jurkat, BCL11B-WT, DMSO, rep1, ATAC
GSM9624241 Jurkat, BCL11B-WT, DMSO, rep2, ATAC
GSM9624242 Jurkat, BCL11B-WT, dTAGV-1, rep1, ATAC
GSM9624243 Jurkat, BCL11B-WT, dTAGV-1, rep2, ATAC
GSM9624244 Jurkat, BCL11B-dTAG, DMSO, rep1, ATAC
GSM9624245 Jurkat, BCL11B-dTAG, DMSO, rep2, ATAC
GSM9624246 Jurkat, BCL11B-dTAG, dTAGV-1, rep1, ATAC
GSM9624247 Jurkat, BCL11B-dTAG, dTAGV-1, rep2, ATAC

Datasets on a similar topic

GSE327367 Motif-directed chromatin repression by BCL11B shapes ectopic targeting and lineage commitment 76 samples shares bcl11b, motif-directed, repression, commitment, chromatin, targeting, ectopic
GSE327361 Motif-directed chromatin repression by BCL11B shapes ectopic targeting and lineage commitment [RNA-seq] 16 samples shares bcl11b, motif-directed, repression, commitment, chromatin, targeting, ectopic
GSE323137 Targeting the CHD3 Chromatin Remodeler Exploits a Synthetic Lethal Vulnerability in SWI/SNF-Deficient Cancers via Toxic Derepression of PARD3B 39 samples shares repression, chromatin, targeting
GSE306350 GSX2 Regulates Progenitor Maturation and Regional Identity Through Transcriptional Repression in the Developing Basal Ganglia [ATAC-seq] 36 samples shares repression, atac-seq
GSE284553 CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias [ATAC-Seq] 22 samples shares repression, atac-seq
GSE337274 Pioneer transcription factor TAL1 reshapes chromatin architecture to direct erythroid cell fate commitment [CUT&Tag] 21 samples shares commitment, chromatin
GSE270184 Cis-regulatory chromatin loops analysis identifies GRHL3 as a master regulator of surface epithelium commitment 16 samples shares commitment, chromatin
GSE271459 Transcription factor network dynamics during the commitment to oncogene-induced senescence [ATAC-Seq] 12 samples shares commitment, atac-seq

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