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ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency [ChIP-seq]

GSE270784 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 107 samples Submitted 2024/08/20 Platform GPL24676Platform GPL20795Platform GPL34281Platform GPL20301
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 107 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
107 samples: 36 conditions, mostly in duplicateGroups 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
ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotencyNature communications · 2024
Summary (written by the submitters)
The primed epiblast acts as a transitional stage between the relatively homogeneous naïve epiblast and the gastrulating embryo. Its formation entails coordinated changes in regulatory circuits driven by strict epigenetic mechanisms. Using a multi-omic approach in human embryonic stem cell models across the spectrum of peri-implantation development, we demonstrate that the transcription factors ZIC2 and ZIC3 have overlapping but essential roles in opening primed-specific enhancers.
Read the full summary ↓
Together they are essential to facilitate progression to and maintain primed pluripotency. ZIC2/3 achieve their function by recruiting SWI/SNF to chromatin and loss of ZIC2/3 or degradation of SWI/SNF both prevent enhancer activation. Loss of ZIC2/3 results in transcriptome changes consistent with perturbed Polycomb activity and a shift towards the expression of genes linked to mesendoderm differentiation. Additionally, we find an intriguing dependency on the transcriptional machinery for sustained recruitment of ZIC2/3 over a subset of primed-hESC specific enhancers. Taken together, ZIC2 and ZIC3 regulate highly dynamic lineage-specific enhancers and collectively act as key regulators of human primed pluripotency.
Published in
ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency
Hossain I, Priam P, Reynoso SC et al. · Nature communications 2024 · PMID 39358345 · doi:10.1038/s41467-024-52431-1
This dataset
Open GSE270784 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 GSE270784_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 PRJNA1128168 and SRA study SRP516114. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39358345) ↗
Study design
36 conditions, mostly in duplicate
UCLA1 primed hESC, Input, ×5 UCLA1 primed hESC, ZIC2 ChIP-seq, ×4 UCLA1 primed hESC, IgG ChIP-seq, ×4 UCLA1 primed hESC, NT control, H3K27me3 ChIP-… ×4 UCLA1 primed hESC, NT control, Input, ×4 UCLA1 primed hESC, ZIC2-/-, H3K27me3 ChIP-seq, ×3 UCLA1 primed hESC, ZIC2-/-, Input, ×3 UCLA1 naïve hESC, Inducible ZIC2 DOX 0h, H3K2… ×2 +50 more

Supports a between-group comparison across 85 samples.

How we read this: 36 replicated groups read from 107 sample titles; they account for 85 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

+ 67 more — browse all 107 samples with per-sample file links →

Datasets on a similar topic

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