GEO series

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

GSE327361 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2026/04/09 Platform GPL11154Platform GPL34284

At a glance

RNA-seq (gene expression) · human · 16 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 16 samples: 16 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 GSE327361 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 GSE327361_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1450594 and SRA study SRP690184. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

16 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 16 sample titles: 16 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

GSM9624248 CD34, empty vector, DMSO, rep1, RNA
GSM9624249 CD34, empty vector, DMSO, rep2, RNA
GSM9624250 CD34, empty vector, DMSO, rep3, RNA
GSM9624251 CD34, empty vector, dTAGV-1, rep1, RNA
GSM9624252 CD34, empty vector, dTAGV-1, rep2, RNA
GSM9624253 CD34, empty vector, dTAGV-1, rep3, RNA
GSM9624254 CD34, BCL11B-dTAG, DMSO, rep1, RNA
GSM9624255 CD34, BCL11B-dTAG, DMSO, rep2, RNA
GSM9624256 CD34, BCL11B-dTAG, DMSO, rep3, RNA
GSM9624257 CD34, BCL11B-dTAG, dTAGV-1, rep1, RNA
GSM9624258 CD34, BCL11B-dTAG, dTAGV-1, rep2, RNA
GSM9624259 CD34, BCL11B-dTAG, dTAGV-1, rep3, RNA
GSM9624260 Jurkat, BCL11BdTAG, DMSO, rep1, RNA
GSM9624261 Jurkat, BCL11BdTAG, DMSO, rep2, RNA
GSM9624262 Jurkat, BCL11BdTAG, dTAGV-1, rep1, RNA
GSM9624263 Jurkat, BCL11BdTAG, dTAGV-1, rep2, RNA

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, lineage
GSE327360 Motif-directed chromatin repression by BCL11B shapes ectopic targeting and lineage commitment [ATAC-seq] 20 samples shares bcl11b, motif-directed, repression, commitment, chromatin, targeting, ectopic, lineage
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
GSE254242 Cancer cell type-specific derepression of transposable elements by inhibition of chromatin modifier enzymes [RNA-Seq] 99 samples shares repression, chromatin
GSE267992 Mutant GFAP alters lineage commitment of neural organoids 79 samples shares commitment, lineage
GSE263193 Cardiac differentiation roadmap for analysis of plasticity and balanced lineage commitment 63 samples shares commitment, lineage
GSE303838 MECP2 Mutations Rewire Human ESC Fate and Bias Cortical Lineage Commitment [RNA-Seq] 48 samples shares commitment, lineage
GSE267990 Mutant GFAP alters lineage commitment of neural organoids [AxDorganoids_bulk_experiment2] 47 samples shares commitment, lineage

Search all human RNA-seq datasets in GEO →

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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.