GEO series

Somatic mutations reveal the ontogeny of microglia in human aging [snATAC-seq]

GSE338484 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 29 samples Submitted 2026/07/13 Platform GPL34284

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 29 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: 29 samples: 20 × UWGroups 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)

Microglia are the resident macrophages of the central nervous system. In mice, microglia seed the brain during embryogenesis and can be maintained throughout life with minimal input from adult hematopoiesis. The origins of human microglia are less clear, but recent evidence suggests that marrow-derived cells contribute to the human microglial pool in certain individuals.

Read the full summary ↓

Here, to investigate the ontogeny of human microglia, we develop a method that uses the collection of accumulated somatic mutations which uniquely labels each clone of cells to track the infiltration of marrow-derived cells into the human brain. Applying this method to 20 aged individuals, we find evidence of an influx of marrow-derived cells into the brain in all examined individuals. Single cell analysis, including single cell lineage tracing using mitochondrial DNA variants, demonstrates that these infiltrating cells are similar to microglia and can comprise a large fraction of the microglial pool. Analysis of large-scale sequencing cohorts demonstrates a protective association between most types of clonal hematopoiesis and Alzheimer’s disease. In sum, this work uncovers a widespread influx of myeloid cells into the healthy human brain which contributes to the pool of human microglia and becomes common with aging.

This dataset

Open GSE338484 in finder → Find more human 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 GSE338484_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 PRJNA1494556 and SRA study SRP717695. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

20 × UW

Supports a between-group comparison across 20 samples.

How we read this: 1 replicated groups read from 29 sample titles; they account for 20 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

GSM9875058 UW1 UW
GSM9875060 UW2 UW
GSM9875061 UW3 UW
GSM9875062 UW4_v2
GSM9875063 UW5 UW
GSM9875064 UW6_v2
GSM9875065 UW6_Ce
GSM9875066 UW6_Pu
GSM9875067 UW7 UW
GSM9875068 UW8 UW
GSM9875070 UW9 UW
GSM9875071 UW9_Pu
GSM9875072 UW10 UW
GSM9875073 UW11 UW
GSM9875074 UW12 UW
GSM9875075 UW13 UW
GSM9875076 UW14 UW
GSM9875077 UW15 UW
GSM9875078 UW15_Pu
GSM9875080 UW16_v2
GSM9875081 UW16_Ce
GSM9875082 UW16_Pu
GSM9875083 UW17 UW
GSM9875084 UW18 UW
GSM9875085 UW19 UW
GSM9875086 UW20 UW
GSM9875087 UW21 UW
GSM9875088 UW22 UW
GSM9875089 UW23 UW

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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.