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Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues

GSE278007 Mus musculus (mouse) Other 18 samples Submitted 2025/05/19 Platform GPL34284Platform GPL34290
At a glance

mouse · 18 samples

Organism
Mus musculus (mouse)
Samples
18 samples: 7 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.
Paper
Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissuesNature communications · 2025
Summary (written by the submitters)
Despite the extensive collection of formalin-fixed paraffin-embedded (FFPE) specimens, molecular tools for their in-depth analysis remain limited. Here, we introduce spatial FFPE-ATAC-seq, a technique that enables chromatin accessibility profiling in archival FFPE tissues with spatial resolution. Applied to both human and mouse samples, this method revealed the complex spatial organization and distinct cellular architectures, unlocking the potential of FFPE samples for comprehensive epigenomic studies and human disease research.
Published in
Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues
Guo P, Chen Y, Mao L et al. · Nature communications 2025 · PMID 40595535 · doi:10.1038/s41467-025-60882-3
This dataset
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Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗
3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE278007_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA1165212. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40595535) ↗
Study design
7 conditions, mostly in duplicate
FF_ATAC_Mouse_brain_50um ×3 FFPE_ATAC_Mouse_brain_50um_S4 ×2 FFPE_ATAC_Mouse_brain_50um_S5 ×2 FFPE_ATAC_Mouse_brain_50um_S6 ×2 FFPE_ATAC_Mouse_brain_50um_S7 ×2 FFPE_ATAC_Mouse_brain_50um_S8 ×2 FFPE_ATAC_Human_thymus_50um ×2 FFPE_ATAC_Human_cerebellum_50um ×1 +2 more

Supports a between-group comparison across 15 samples.

How we read this: 7 replicated groups read from 18 sample titles; they account for 15 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
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