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Epigenetic and 3D genome reprogramming during the aging of human hippocampus

GSE278576 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 80 samples Submitted 2024/12/05 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 80 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
Homo sapiens (human)
Samples
80 samples: 80 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.
Paper
Epigenetic and 3D genome reprogramming during the aging of human hippocampusbioRxiv : the preprint server for biology · 2024
Summary (written by the submitters)
Age-related cognitive decline in humans is associated with altered physiology of the hippocampus, a region critical for memory consolidation and spatial navigation. While changes in gene expression have been observed in aging brain cells, our understanding of the regulatory mechanisms underlying these changes and their connection to chromatin structure remains limited.
Read the full summary ↓
To unravel these complexities, we have applied a comprehensive multi-omics approach, integrating single-nucleus gene expression, chromatin accessibility, DNA methylation, and 3D chromatin architecture data obtained from the hippocampi of 40 neurotypical human donors spanning the adult lifespan. We observed a striking loss of astrocytes, oligodendrocyte precursor cells, and endothelial cells during aging. In particular, we observed a substantial decline in the subset of astrocytes that play a role in maintaining and regulating synaptic transmission. In addition, microglia undergo a dramatic switch from a predominantly homeostatic state to an epigenetically primed inflammatory state that coincides with reprogramming of their DNA methylomes and activation of endogenous retrotransposons. In the aged cells, we detected erosion of the 3D genome architecture, where local chromatin domains are diminished and trans-chromosomal interactions are strengthened. Importantly, age-related changes in chromatin folding have high correspondence with the transcriptome and epigenome in multiple cell types. Our data identifies age-associated changes in cell types/states and gene regulatory features that provide insight into the loss of synapses and cognitive decline that occurs in the human brain during aging.
Published in
Epigenetic and 3D genome reprogramming during the aging of human hippocampus
Zemke NR, Lee S, Mamde S et al. · bioRxiv : the preprint server for biology 2024 · PMID 39463924 · doi:10.1101/2024.10.14.618338
This dataset
Open GSE278576 in finder → Find more human 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 GSE278576_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 PRJNA1167280 and SRA study SRP535909. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39463924) ↗
Study design
80 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 80 sample titles: 80 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

+ 40 more — browse all 80 samples with per-sample file links →

Datasets on a similar topic

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