GEO series

Developmental cell type specific enhancers in orofacial morphology and disease [mouse]

GSE249496 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 24 samples Submitted 2025/12/01 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 24 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: 24 samples: 24 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)

The noncoding genome contains sequences called enhancers which facilitate expression of target genes through recruitment and binding of transcription factors. Enhancers are typically active in developmental stage-, tissue-, and cell type-specific patterns, whereby they control the spatiotemporal expression patterns of target genes. Sequence variation within enhancers can alter expression of their target genes where the enhancer is active, causing isolated phenotypes ranging from normal morphological differences to malformations.

Read the full summary ↓

The role of orofacial enhancers in normal morphology and disease of the orofacial region has previously been established in bulk human assays. However, the conservation of these findings and the cell types contributing to these phenotypes are unknown, limiting work in prevention and treatment of malformations. To uncover cell type-specific enhancers whose sequence variants contribute to normal facial morphology and malformations, we performed single cell multiome (snATAC and snRNA-seq) sequencing on 17 human samples spanning 6 unique stages from 4-8 weeks gestation and 14 mouse samples spanning 6 stages from E9.5-15.5. We identified 15 distinct cell types, for which we leveraged the cell type specific chromatin accessibility and transcriptomic profiles and previously published chromatin conformation data to identify cell type specific enhancer-gene predicted interactions, which we call the ‘enhancerprints’. These enhancerprints revealed a cell type-specific enrichment pattern of common single nucleotide variants for biologically relevant phenotypes such as epithelium in orofacial clefting and mesenchyme in facial variation.

This dataset

Open GSE249496 in finder → Find more mouse 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 GSE249496_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 PRJNA1049388 and SRA study SRP476161. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

24 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 24 sample titles: 24 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

GSM7949015 Embryonic day 9.5 primary mouse orofacial prominences, replicate #1 [snRNA-seq GEX]
GSM7949016 Embryonic day 9.5 primary mouse orofacial prominences, replicate #1 [snATAC-seq]
GSM7949017 Embryonic day 9.5 primary mouse orofacial prominences, replicate #2 [snRNA-seq GEX]
GSM7949018 Embryonic day 9.5 primary mouse orofacial prominences, replicate #2 [snATAC-seq]
GSM7949019 Embryonic day 9.5 primary mouse orofacial prominences, replicate #3 [snRNA-seq GEX]
GSM7949020 Embryonic day 9.5 primary mouse orofacial prominences, replicate #3 [snATAC-seq]
GSM7949021 Embryonic day 10.5 primary mouse orofacial prominences, replicate #1 [snRNA-seq GEX]
GSM7949022 Embryonic day 10.5 primary mouse orofacial prominences, replicate #1 [snATAC-seq]
GSM7949023 Embryonic day 10.5 primary mouse orofacial prominences, replicate #2 [snRNA-seq GEX]
GSM7949024 Embryonic day 10.5 primary mouse orofacial prominences, replicate #2 [snATAC-seq]
GSM7949025 Embryonic day 10.5 primary mouse orofacial prominences, replicate #3 [snRNA-seq GEX]
GSM7949026 Embryonic day 10.5 primary mouse orofacial prominences, replicate #3 [snATAC-seq]
GSM7949027 Embryonic day 11.5 primary mouse orofacial prominences, replicate #1 [snRNA-seq GEX]
GSM7949028 Embryonic day 11.5 primary mouse orofacial prominences, replicate #1 [snATAC-seq]
GSM7949029 Embryonic day 11.5 primary mouse orofacial prominences, replicate #2 [snRNA-seq GEX]
GSM7949030 Embryonic day 11.5 primary mouse orofacial prominences, replicate #2 [snATAC-seq]
GSM7949031 Embryonic day 11.5 primary mouse orofacial prominences, replicate #3 [snRNA-seq GEX]
GSM7949032 Embryonic day 11.5 primary mouse orofacial prominences, replicate #3 [snATAC-seq]
GSM7949033 Embryonic day 12.5 primary mouse orofacial prominences, replicate #1 [snRNA-seq GEX]
GSM7949034 Embryonic day 12.5 primary mouse orofacial prominences, replicate #1 [snATAC-seq]
GSM7949035 Embryonic day 12.5 primary mouse orofacial prominences, replicate #2 [snRNA-seq GEX]
GSM7949036 Embryonic day 12.5 primary mouse orofacial prominences, replicate #2 [snATAC-seq]
GSM7949037 Embryonic day 12.5 primary mouse orofacial prominences, replicate #3 [snRNA-seq GEX]
GSM7949038 Embryonic day 12.5 primary mouse orofacial prominences, replicate #3 [snATAC-seq]

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