GEO series

Comprehensive single-cell transcriptomic profiling of the scalp from patients with moderate-to-severe alopecia areata

GSE316832 Homo sapiens (human) Single-cell RNA-seq 30 samples Submitted 2026/03/16 Platform GPL34281

At a glance

Single-cell RNA-seq · human · 30 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 30 samples: 30 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: Comprehensive single-cell transcriptomic profiling of the scalp from patients with moderate-to-severe alopecia areataThe Journal of allergy and clinical immunology · 2026

Summary (written by the submitters)

Background: Alopecia areata (AA) is an autoimmune hair loss disorder characterized by follicular destruction. While bulk transcriptomic studies have identified contributory inflammatory axes, specific cell pathways remain underexplored. Objective: To characterize the single-cell transcriptomic landscape underpinning AA scalp compared to healthy controls.

Read the full summary ↓

Methods: We performed single-cell RNA-sequencing on lesional and nonlesional scalp biopsies from 13 patients with moderate-to-severe AA (5 with alopecia totalis/universalis [AT/AU]) and 11 healthy controls. Results: Overall, we profiled 41,067 high-quality cells. Lesional AA samples demonstrated robust Th1 activation and cytotoxicity, with upregulated IFNG, GZMH/K, and XCL1/2. Concurrently, Th2 skewing (IL13, IL13RA1, IL4R) and TNFRSF4/OX40 elevations in lesional CD4+ and regulatory T-cells were also observed. IL15, JAK2/3, and STAT1 levels were increased in distinct lesional dendritic cell subsets, with JAK/STAT genes also upregulated in fibroblasts and keratinocytes. Fibroblasts and smooth muscle cells exhibited enriched pro-inflammatory and pro-fibrotic markers (CXCL9, CCL26, POSTN, COL5A3, COL6A6). Lesional keratinocytes further demonstrated downregulated hair keratins and increased interferon signaling. AA endothelial cells showed increased angiogenic and interferon signatures. Compared to patchy AA and controls, AT/AU demonstrated higher expression of multiple cytotoxic, Th1, Th2, and JAK/STAT markers in immune cells, and proliferative and inflammatory signatures in non-immune cells. Conclusion: This comprehensive high-resolution single-cell map uncovers potential communication networks between immune and non-immune cell populations in AA scalp, possibly disrupting immune privilege at the hair follicle and driving disease progression and/or severity. Clinical Implications: These data provide single-cell-resolution insights into AA pathogenesis and potential molecular targets for precision therapies tailored to AA severity.

Published in

Comprehensive single-cell transcriptomic profiling of the scalp from patients with moderate-to-severe alopecia areata

Hu BD, He H, Bose S et al. · The Journal of allergy and clinical immunology 2026 · PMID 41740930 · doi:10.1016/j.jaci.2026.02.014

This dataset

Open GSE316832 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 GSE316832_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1404311 and SRA study SRP663899. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41740930) ↗

Study design

30 samples, each with a distinct title — no replicated groups

Supports a case/control comparison: 19 samples read as cases, 11 as controls.

How we read this: Read from 30 sample titles: 30 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

GSM9460802 Sample 1, healthy control scalp
GSM9460803 Sample 2, healthly control scalp
GSM9460804 Sample 3, healthy control scalp
GSM9460805 Sample 4, healthly control scalp
GSM9460806 Sample 5, healthy control scalp
GSM9460807 Sample 6, healthy control scalp
GSM9460808 Sample 7, healthy control scalp
GSM9460809 Sample 8, healthy control scalp
GSM9460810 Sample 9, healthy control scalp
GSM9460811 Sample 10, healthy control scalp
GSM9460812 Sample 11, healthy control scalp
GSM9460813 Sample 12, nonlesional scalp
GSM9460814 Sample 13, nonlesional scalp
GSM9460815 Sample 14, nonlesional scalp
GSM9460816 Sample 15, nonlesional scalp
GSM9460817 Sample 16 nonlesional scalp
GSM9460818 Sample 17, nonlesional scalp
GSM9460819 Sample 18, nonlesional scalp
GSM9460820 Sample 19, lesional scalp
GSM9460821 Sample 20, lesional scalp
GSM9460822 Sample 21, lesional scalp
GSM9460823 Sample 22, lesional scalp
GSM9460824 Sample 23, lesional scalp
GSM9460825 Sample 24, lesional scalp
GSM9460826 Sample 25, lesional scalp
GSM9460827 Sample 26, lesional scalp
GSM9460828 Sample 27, lesional scalp
GSM9460829 Sample 28, lesional scalp
GSM9460830 Sample 29, lesional scalp
GSM9460831 Sample 30, lesional scalp

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