GEO series

SALL4 recruits BAF to activate enhancers required for cranial neural crest cell specification

GSE293821 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 26 samples Submitted 2025/04/08 Platform GPL30173Platform GPL34284

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 26 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: 26 samples: 26 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.
Paper: Neural crest induction requires SALL4-mediated BAF recruitment to lineage specific enhancersDevelopment (Cambridge, England) · 2025

Summary (written by the submitters)

SALL4 is a critical transcription factor involved in early embryonic development. While its role in pluripotency remains debated, SALL4 has been implicated in various lineage specification processes. The neural crest-derived anomalies observed in individuals with SALL4 haploinsufficiency, combined with high SALL4 expression observed in mouse cranial neural crest cells (CNCCs), suggest a role for this transcription factor in CNCC specification and craniofacial development, however, this has not yet been investigated.

Read the full summary ↓

Moreover, while SALL4 is an established interactor of the NuRD chromatin remodeling complex, recent mass-spectrometry studies from our group have suggested a novel interaction between SALL4 and the BAF complex during human CNCC specification. Here, we investigate the functional significance of this interaction and the broader role of SALL4 in CNCC development. We generated a human iPSC line with SALL4 heterozygous knock-out to model the haploinsufficient variants observed in SALL4-associated human developmental syndromes. Our findings reveal that the SALL4A isoform directly interacts with the BAF subunit DPF2 via its zinc-finger-cluster-3 and -4 domain. During early CNCC specification, SALL4A is required for BAF-mediated chromatin remodeling at enhancers essential for CNCC fate. In the absence of SALL4A, cells progress normally through the neuroectodermal stage but fail to specify into CNCCs, as CNCC lineage-specific enhancers remain repressed. Moreover, we demonstrate that the SALL4B isoform cannot compensate for SALL4A loss, as it lacks the zinc-finger-3 domain necessary for BAF interaction. These findings establish a novel role for SALL4A in CNCC specification by regulating BAF-mediated enhancer activation, shedding light on the molecular mechanisms underlying SALL4-associated craniofacial anomalies.

Published in

Neural crest induction requires SALL4-mediated BAF recruitment to lineage specific enhancers

Demurtas M, Barnada SM, van Domselaar E et al. · Development (Cambridge, England) 2025 · PMID 41312722 · doi:10.1242/dev.205248

This dataset

Open GSE293821 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 GSE293821_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 PRJNA1246518 and SRA study SRP576504. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41312722) ↗

Study design

26 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 26 sample titles: 26 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

GSM8890955 MT770_RNA_seq_SV20_WT_D0_rep1
GSM8890956 MT771_RNA_seq_SV20_SALL4_KO_D0_rep1
GSM8890957 MT772_RNA_seq_SV20_WT_D0_rep2
GSM8890958 MT773_RNA_seq_SV20_SALL4_KO_D0_rep2
GSM8890959 MT850_RNA_seq_SV20_WT_D5_rep1
GSM8890960 MT851_RNA_seq_SV20_SALL4_KO_D5_rep1
GSM8890961 MT852_RNA_seq_SV20_WT_D5_rep2
GSM8890962 MT853_RNA_seq_SV20_SALL4_KO_D5_rep2
GSM8890963 MT854_RNA_seq_SV20_WT_D5_rep3
GSM8890964 MT855_RNA_seq_SV20_SALL4_KO_D5_rep3
GSM8890965 MT856_RNA_seq_SV20_WT_D14_rep1
GSM8890966 MT857_RNA_seq_SV20_SALL4_KO_D14_rep1
GSM8890967 MT858_RNA_seq_SV20_WT_D14_rep2
GSM8890968 MT859_RNA_seq_SV20_SALL4_KO_D14_rep2
GSM8890969 MT669_ATAC_seq_SV20_WT_D0_rep1
GSM8890970 MT748_ATAC_seq_SV20_WT_D0_rep2
GSM8890971 MT673_ATAC_seq_SV20_WT_D5_rep1
GSM8890972 MT674_ATAC_seq_SV20_SALL4_KO_D5_rep1
GSM8890973 MT842_ATAC_seq_SV20_WT_D5_rep2
GSM8890974 MT844_ATAC_seq_SV20_SALL4_KO_D5_rep2
GSM8890975 MT777_CUT_RUN_SALL4_SV20_WT_D0_rep1
GSM8890976 MT829_CUT_RUN_SALL4_SV20_WT_D5_rep1
GSM8890977 MT830_CUT_RUN_SALL4_SV20_WT_D5_rep2
GSM8890978 MT950_ChIP_seq_BRG1_SV20_WT_D5_rep1
GSM8890979 MT952_ChIP_seq_BRG1_SV20_SALL4_KO_D5_rep1
GSM8890980 MT954_ChIP_seq_INPUT_SV20_WT_D5_rep1

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