GEO series

ATAC-seq of mouse cortex undergoing early degradation after traumatic brain injury (TBI)

GSE245683 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 12 samples Submitted 2025/03/06 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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: 12 samples: 3 × ATAC-seq cortex Sham 0h vs 3 × ATAC-seq cortex Sham 2h vs 3 × ATAC-seq cortex TBI 0h vs 3 × ATAC-seq cortex TBI 2hGroups 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)

Advances in molecular diagnostics have enabled accurate disease diagnosis. However, the application of molecular biology technology in the field of forensic medicine, especially in forensic pathology, is still limited. Degraded samples with altered physicochemical properties pose challenges for molecular techniques. Identifying degradation-resistant, sensitive techniques is key for forensic molecular pathology.

Read the full summary ↓

ATAC-seq maps open chromatin and is increasingly used in disease diagnosis and mechanism studies. Given forensic use of degraded DNA, we explored ATAC-seq's potential for analyzing degraded forensic samples. In a TBI model, ATAC-seq detected injury-induced chromatin changes after 2h degradation. We identified 1,432 TBI-associated loci with robust chromatin changes unaffected by degradation. These loci have potential as a panel of biomarkers for molecular diagnosis from degraded forensic samples.

This dataset

Open GSE245683 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 GSE245683_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 PRJNA1029568 and SRA study SRP467094. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × ATAC-seq cortex Sham 0h vs 3 × ATAC-seq cortex Sham 2h vs 3 × ATAC-seq cortex TBI 0h vs 3 × ATAC-seq cortex TBI 2h

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM7846909 ATAC-seq cortex Sham 0h rep1 ATAC-seq cortex Sham 0h
GSM7846910 ATAC-seq cortex Sham 0h rep2 ATAC-seq cortex Sham 0h
GSM7846911 ATAC-seq cortex Sham 0h rep3 ATAC-seq cortex Sham 0h
GSM7846912 ATAC-seq cortex Sham 2h rep1 ATAC-seq cortex Sham 2h
GSM7846913 ATAC-seq cortex Sham 2h rep2 ATAC-seq cortex Sham 2h
GSM7846914 ATAC-seq cortex Sham 2h rep3 ATAC-seq cortex Sham 2h
GSM7846915 ATAC-seq cortex TBI 0h rep1 ATAC-seq cortex TBI 0h
GSM7846916 ATAC-seq cortex TBI 0h rep2 ATAC-seq cortex TBI 0h
GSM7846917 ATAC-seq cortex TBI 0h rep3 ATAC-seq cortex TBI 0h
GSM7846918 ATAC-seq cortex TBI 2h rep1 ATAC-seq cortex TBI 2h
GSM7846919 ATAC-seq cortex TBI 2h rep2 ATAC-seq cortex TBI 2h
GSM7846920 ATAC-seq cortex TBI 2h rep3 ATAC-seq cortex TBI 2h

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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.