GEO series

Limb cell-fate commissioning is guided by widespread coordinated genome detachment from the nuclear lamina [Multiome]

GSE293955 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2026/07/15 Platform GPL34290Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 10 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: 10 samples: 10 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)

Diverse forms of heterochromatin block inappropriate transcription and safeguard differentiation and cell identity. Yet, how and when heterochromatin is reconfigured to facilitate changes in cell-fate remains a key open question. Here, we address this by mapping a prevalent heterochromatic feature - genome-lamina interactions - relative to transcription in single-cells during mouse embryogenesis.

Read the full summary ↓

We find that lamina-genome interactions remain relatively uniform following gastrulation but are extensively reconfigured during organogenesis in diverse tissues. Focusing on limb development, we demonstrate that genome-lamina interactions are selectively released at key developmental genes and their surrounding regulatory domains in early multipotent progenitors. Strikingly, this “lamina-release” often precedes later gene expression, suggesting it primes regulatory domains for future potential activation. Lamina-release also coincides with the putative binding of crucial limb transcription factors and so is closely intertwined with the regulatory machinery that drives limb formation. Conversely, we show that CTCF-defined boundaries of topologically-associated domains (TADs) constrains the spread of lamina-release at a limb gene locus. This ensures independent heterochromatin dynamics between neighbouring domains. Together, this suggests a previously unrecognised process where genome-lamina interactions are selectively dismantled at regulatory domains to transition loci toward more permissive chromatin states, thereby potentiating cell-type specific activation. Our work thus reveals how systematic heterochromatin reorganization links to developmental multipotency, providing mechanistic insight into how progenitors traverse diverse cell-fates in vivo.

This dataset

Open GSE293955 in finder → Find more mouse 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 GSE293955_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 PRJNA1245249 and SRA study SRP575922. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

10 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 10 sample titles: 10 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

GSM8895176 mpimg_L24604-1_ATAC-E8-5
GSM8895177 mpimg_L24606-1_RNA-E8-5
GSM8895178 mpimg_L24605-1_ATAC-E9-5
GSM8895179 mpimg_L24607-1_RNA-E9-5
GSM8895180 mpimg_L26649-1_ATAC-Limbs
GSM8895181 mpimg_L26647-1_RNA-Limbs
GSM8895182 A4490_A4418_09_ATAC_E8-5
GSM8895183 A4490_A4418_21_RNA_B3_E8-5
GSM8895184 A4490_A4418_10_ATAC_C10_E9-5
GSM8895185 A4490_A4418_22_RNA_B4_E9-5

Datasets on a similar topic

GSE331509 Limb cell-fate commissioning is guided by widespread coordinated genome detachment from the nuclear lamina [CUT&Tag] 62 samples shares commissioning, coordinated, widespread, detachment, cell-fate, nuclear, guided
GSE200054 Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia 40 samples shares widespread, guided
GSE27394 Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 29 samples shares widespread, nuclear
GSE27218 Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (RNA-seq) 21 samples shares widespread, nuclear
GSE200051 Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [mRNA retina] 10 samples shares widespread, guided
GSE200053 Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [mRNA sclera] 10 samples shares widespread, guided
GSE27371 Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (Affymetrix) 6 samples shares widespread, nuclear
GSE256314 Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements 223 samples shares widespread

Search all mouse ChIP / ATAC / CUT&Tag 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.