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Single cell sequencing of APECED patient and Healthy control peripheral blood cells

GSE339254 Homo sapiens (human) Single-cell RNA-seq 74 samples Submitted 2026/07/28 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 74 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
74 samples: 35 conditions, mostly in duplicateGroups 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)
10 APECED and 10 Healthy control patients peripheral blood cells isolated for single cell sequencing. scRNA-seq and BCRseq analysis illustrate changes to the composition of the B cell compartment in APECED compared to Healthy control such as a reduction in Naïve B cells and increases to IgM CD27+ CXCR3+ and Class switched atypical B cell subsets with alternative activation (TBX21+ ZEB2+).
This dataset
Open GSE339254 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 GSE339254_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 PRJNA1498038 and SRA study SRP719796. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
35 conditions, mostly in duplicate
Healthy_001_1749853_1_1 ×2 Healthy_001_1749853_2_1 ×2 APECED_003_1749854_1_1 ×2 APECED_003_1749854_2_1 ×2 APECED_001_1753268_2_1 ×2 APECED_002_1760324_1_1 ×2 APECED_002_1760324_2_1 ×2 APECED_004_1767708_1_1 ×2 +31 more

Supports a between-group comparison across 70 samples.

How we read this: 35 replicated groups read from 74 sample titles; they account for 70 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

+ 34 more — browse all 74 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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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.