GEO series

Neocortical temporal patterning by a two-layered regulatory structure

GSE204701 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 26 samples Submitted 2025/05/23 Platform GPL24247Platform GPL21273

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 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: Mus musculus (mouse)
Samples: 26 samples: 13 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.

Summary (written by the submitters)

In the developing neocortex, a diverse array of neurons with defined types and abundances are systematically generated by a limited population of radial glial progenitors (RGPs) as they undergo successive fate changes. How this temporal patterning is regulated at the molecular level remains largely unknown.

Read the full summary ↓

Here we present an in-depth single-cell multi-omics assay for deep characterization of regulatory programs, along with an analytical framework that integrates joint dynamics in single-cell transcription and chromatin structure to interrogate the regulation of temporal identities and fate progression of RGPs. We found that RGP temporal patterning is governed by a two-layered regulatory structure consisting of global regulators acting upon a cascade of transcription factor (TF) hubs. This cascade proceeds not by confining cascaded TF expression to specific temporal windows, but through synergistic transcriptional and epigenetic dynamics that temporally modulate TF regulatory activity. Furthermore, global regulators exhibit a progressively increasing expression pattern, and our computational modeling analysis found that the gradient of this pattern specifies the duration of each cascading stage and, subsequently, the abundance of specific progeny output. Together, this two-layered regulatory structure offers a mechanistic control of temporal patterning and emphasizes the importance of global regulators in managing temporal programs.

This dataset

Open GSE204701 in finder → Find more mouse 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 GSE204701_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 PRJNA841987 and SRA study SRP376857. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

13 conditions, mostly in duplicate

HiC-seq for E10-E11 brain cortex, ×2 HiC-seq for E12-E15 brain cortex, ×2 HiC-seq for E12-E13 brain cortex, ×2 HiC-seq for E14-E15 brain cortex, ×2 H3K27me3 ChIP-seq for E10 brain cortex, ×2 H3K27me3 ChIP-seq for E12 brain cortex, ×2 H3K27ac ChIP-seq for E10 brain cortex, ×2 H3K27ac ChIP-seq for E12 brain cortex, ×2 +5 more

Supports a between-group comparison across 26 samples.

How we read this: 13 replicated groups read from 26 sample titles; they account for 26 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

GSM6186017 HiC-seq for E10-E11 brain cortex, rep1 HiC-seq for E10-E11 bra…
GSM6186018 HiC-seq for E10-E11 brain cortex, rep2 HiC-seq for E10-E11 bra…
GSM6186019 HiC-seq for E12-E15 brain cortex, rep1 HiC-seq for E12-E15 bra…
GSM6186020 HiC-seq for E12-E15 brain cortex, rep2 HiC-seq for E12-E15 bra…
GSM7157501 HiC-seq for E12-E13 brain cortex, rep1 HiC-seq for E12-E13 bra…
GSM7157502 HiC-seq for E14-E15 brain cortex, rep1 HiC-seq for E14-E15 bra…
GSM7157503 H3K27me3 ChIP-seq for E10 brain cortex, rep1 H3K27me3 ChIP-seq for E…
GSM7157504 H3K27me3 ChIP-seq for E12 brain cortex, rep1 H3K27me3 ChIP-seq for E…
GSM7157505 H3K27ac ChIP-seq for E10 brain cortex, rep1 H3K27ac ChIP-seq for E1…
GSM7157506 H3K27ac ChIP-seq for E12 brain cortex, rep1 H3K27ac ChIP-seq for E1…
GSM7157507 Input ChIP-seq for brain cortex, rep1 Input ChIP-seq for brai…
GSM7157508 H3K27me3 CUT&Tag for E12-E13 brain cortex, rep1 H3K27me3 CUT&Tag for E1…
GSM7157509 H3K27me3 CUT&Tag for E14-E15 brain cortex, rep1 H3K27me3 CUT&Tag for E1…
GSM7157510 H3K27ac CUT&Tag for E12-E13 brain cortex, rep1 H3K27ac CUT&Tag for E12…
GSM7157511 H3K27ac CUT&Tag for E14-E15 brain cortex, rep1 H3K27ac CUT&Tag for E14…
GSM7157512 HiC-seq for E12-E13 brain cortex, rep2 HiC-seq for E12-E13 bra…
GSM7157513 HiC-seq for E14-E15 brain cortex, rep2 HiC-seq for E14-E15 bra…
GSM7157514 H3K27me3 ChIP-seq for E10 brain cortex, rep2 H3K27me3 ChIP-seq for E…
GSM7157515 H3K27me3 ChIP-seq for E12 brain cortex, rep2 H3K27me3 ChIP-seq for E…
GSM7157516 H3K27ac ChIP-seq for E10 brain cortex, rep2 H3K27ac ChIP-seq for E1…
GSM7157517 H3K27ac ChIP-seq for E12 brain cortex, rep2 H3K27ac ChIP-seq for E1…
GSM7157518 Input ChIP-seq for brain cortex, rep2 Input ChIP-seq for brai…
GSM7157519 H3K27me3 CUT&Tag for E12-E13 brain cortex, rep2 H3K27me3 CUT&Tag for E1…
GSM7157520 H3K27me3 CUT&Tag for E14-E15 brain cortex, rep2 H3K27me3 CUT&Tag for E1…
GSM7157521 H3K27ac CUT&Tag for E12-E13 brain cortex, rep2 H3K27ac CUT&Tag for E12…
GSM7157522 H3K27ac CUT&Tag for E14-E15 brain cortex, rep2 H3K27ac CUT&Tag for E14…

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