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Modeling Hereditary Diffuse Leukoencephalopathy with Axonal Spheroids using microglia-sufficient brain organoids

GSE271810 Homo sapiens (human) RNA-seq (gene expression) 32 samples Submitted 2024/12/31 Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 32 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
32 samples: 6 conditions, mostly in triplicateGroups 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
Modeling hereditary diffuse leukoencephalopathy with axonal spheroids using microglia-sufficient brain organoidseLife · 2025
Summary (written by the submitters)
Hereditary diffuse leukoencephalopathy with axonal spheroids (HDLS) is a rare, fatal, adult-onset neurodegenerative disease that is most often caused by mutations affecting the Colony Stimulating factor-1 Receptor (CSF-1R).
Read the full summary ↓
To understand how CSF-1R-mutation affects human microglia – the specialized brain-resident macrophages of the central nervous system – and the downstream consequences for neuronal cells, we used a macrophage and forebrain organoid co-culture system based on induced pluripotent stem cells generated from two patients with HDLS, with CSF-1R gene-corrected isogenic organoids as controls. Macrophages derived from iPSC (iMacs) of patients exhibited a metabolic shift towards the glycolytic pathway and reduced CSF-1 sensitivity, which was associated with higher levels of IL-1β production and an activated inflammatory phenotype. Bulk RNA sequencing revealed that iMacs adopt a reactive state that leads to impaired regulation of neuronal cell populations in organoid cultures, thereby identifying microglial dysregulation and specifically IL-1β production as key contributors to the degenerative neuro-environment in HDLS.
Published in
Modeling hereditary diffuse leukoencephalopathy with axonal spheroids using microglia-sufficient brain organoids
Wong WJ, Zhu YW, Wang HT et al. · eLife 2025 · PMID 40397490 · doi:10.7554/eLife.96693
This dataset
Open GSE271810 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 GSE271810_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1133661 and SRA study SRP518798. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40397490) ↗
Study design
6 conditions, mostly in triplicate
Mut_HD2_iMac ×4 IsoHD2_iMac ×4 Mut_HD1_iMac ×3 IsoHD1_iMac ×3 HD1_iMicroglia ×3 HD2_iMicroglia ×3 HD2_co-culture_neurons_1(IsoHD2_Org_Mut_HD2_i… ×1 HD2_co-culture_neurons_2(IsoHD2_Org_Mut_HD2_i… ×1 +10 more

Supports a between-group comparison across 20 samples.

How we read this: 6 replicated groups read from 32 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
Datasets on a similar topic

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