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Type 2 cytokine-dependent skin barrier regulation in personalized 2D- and 3D skin models of atopic dermatitis: A pilot study

GSE243634 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2024/08/19 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 16 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
16 samples: 4 × SAMPLE_00000001_R01_C vs 4 × SAMPLE_00000001_R02_C vs 4 × SAMPLE_00000002_R03_C vs 4 × SAMPLE_00000002_R04_CGroups 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
Type 2 Cytokine-Dependent Skin Barrier Regulation in Personalized 2-Dimensional and 3-Dimensional Skin Models of Atopic Dermatitis: A Pilot StudyJID innovations : skin science from molecules to population health · 2025
Summary (written by the submitters)
Keratinocytes from healthy donors stimulated with type 2 cytokines are often used to experimentally study atopic dermatitis (AD) inflammatory responses. Due to potential intrinsic alterations, it seems favorable to use keratinocytes from AD patients. Keratinocytes isolated from hair follicles offer a non-invasive approach to investigate AD-derived keratinocytes.
Read the full summary ↓
To evaluate whether such AD-derived keratinocytes are suitable to mimic AD inflammatory responses we compared hair follicle-derived keratinocytes from healthy donors and AD patients in a type 2 cytokine environment. Stimulation of AD-derived keratinocytes with IL-4 and IL-13 induced higher expression changes of AD-associated markers as compared to healthy keratinocytes. The combination of IL-4 and IL-13 generally induced highest expression changes, but IL-13 alone also induced significant changes of AD-specific markers. Similar to the 2D cultures, IL-4/IL-13 stimulation of 3D skin models generated with AD-derived keratinocytes modulated the expression of several AD-relevant factors. Whole transcriptome analysis revealed that IL-4 and IL-13 acted similarly on these 3D skin models. Histologically, IL-13 alone and in combination with IL-4 increased epidermal spongiosis, a histological hallmark of AD skin. Taken together, our pilot study suggests that hair follicle-derived keratinocytes from AD patients represent a useful model system to study AD-related inflammation in a personalized in vitro model.
Published in
Type 2 Cytokine-Dependent Skin Barrier Regulation in Personalized 2-Dimensional and 3-Dimensional Skin Models of Atopic Dermatitis: A Pilot Study
Emmert H, Rademacher F, Hübenthal M et al. · JID innovations : skin science from molecules to population health 2025 · PMID 39385749 · doi:10.1016/j.xjidi.2024.100309
This dataset
Open GSE243634 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 GSE243634_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 PRJNA1019296 and SRA study SRP462119. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39385749) ↗
Study design
4 × SAMPLE_00000001_R01_C vs 4 × SAMPLE_00000001_R02_C vs 4 × SAMPLE_00000002_R03_C vs 4 × SAMPLE_00000002_R04_C

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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
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