GEO series

Human keratinocytes and fibroblasts coordinate early cutaneous innate defense against Candida auris

GSE334767 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2026/06/12 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 24 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: 24 samples: 6 conditions, mostly with about 4 replicates eachGroups 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)

Candida auris (C. auris) is an emerging fungal pathogen with a remarkable ability to persist on human skin, but how structural skin cells respond to colonization is unclear. We used ex vivo human skin models, primary keratinocytes and fibroblasts to characterize epithelial and stromal responses to C. auris compared with Candida albicans (C.

Read the full summary ↓

albicans). C. auris formed biofilms and induced a wound-model-dependent pattern of cytokine secretion dominated by IL-1β and IL-6, yet caused minimal epithelial damage and modest reductions in leukocyte viability. RNA sequencing revealed complementary but cell-type-specific responses. Keratinocytes and fibroblasts both amplified a pro-inflammatory IL-6/CXCL8 response, while keratinocytes additionally upregulated antimicrobial genes such as RNASE7, TSLP, DEFB103A, and the neutrophil-recruiting chemokines CXCL2 and CXCL3. Fibroblasts further induced CCL28, supporting T-cell recruitment, alongside transcriptional programs associated with tissue remodeling. Recombinant RNase 7 and short form TSLP directly inhibited C. auris growth in vitro in a dose-dependent manner. Together, these findings identify keratinocytes as epithelial sentinels that integrate inflammatory and antimicrobial defenses against skin-tropic C. auris and suggest that fibroblast-driven cytokine amplification and especially antimicrobial peptides from within the skin barrier may provide therapeutic targets to limit C. auris skin colonization.

This dataset

Open GSE334767 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 GSE334767_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 PRJNA1476316 and SRA study SRP708221. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly with about 4 replicates each

Keratinocyte, PBS control, ×4 Keratinocyte, Strain 48, ×4 Keratinocyte, Strain 47, ×4 Fibroblast, PBS control, ×4 Fibroblast, Strain 48, ×4 Fibroblast, Strain 47, ×4

Supports a between-group comparison across 24 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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

GSM9796811 Keratinocyte, PBS control, replicate 1 Keratinocyte, PBS contr…
GSM9796812 Keratinocyte, Strain 48, replicate 1 Keratinocyte, Strain 48,
GSM9796813 Keratinocyte, Strain 47, replicate 1 Keratinocyte, Strain 47,
GSM9796814 Keratinocyte, PBS control, replicate 2 Keratinocyte, PBS contr…
GSM9796815 Keratinocyte, Strain 48, replicate 2 Keratinocyte, Strain 48,
GSM9796816 Keratinocyte, Strain 47, replicate 2 Keratinocyte, Strain 47,
GSM9796817 Keratinocyte, PBS control, replicate 3 Keratinocyte, PBS contr…
GSM9796818 Keratinocyte, Strain 48, replicate 3 Keratinocyte, Strain 48,
GSM9796819 Keratinocyte, Strain 47, replicate 3 Keratinocyte, Strain 47,
GSM9796820 Keratinocyte, PBS control, replicate 4 Keratinocyte, PBS contr…
GSM9796821 Keratinocyte, Strain 48, replicate 4 Keratinocyte, Strain 48,
GSM9796822 Keratinocyte, Strain 47, replicate 4 Keratinocyte, Strain 47,
GSM9796823 Fibroblast, PBS control, replicate 1 Fibroblast, PBS contro…
GSM9796824 Fibroblast, Strain 48, replicate 1 Fibroblast, Strain 48,
GSM9796825 Fibroblast, Strain 47, replicate 1 Fibroblast, Strain 47,
GSM9796826 Fibroblast, PBS control, replicate 2 Fibroblast, PBS contro…
GSM9796827 Fibroblast, Strain 48, replicate 2 Fibroblast, Strain 48,
GSM9796828 Fibroblast, Strain 47, replicate 2 Fibroblast, Strain 47,
GSM9796829 Fibroblast, PBS control, replicate 3 Fibroblast, PBS contro…
GSM9796830 Fibroblast, Strain 48, replicate 3 Fibroblast, Strain 48,
GSM9796831 Fibroblast, Strain 47, replicate 3 Fibroblast, Strain 47,
GSM9796832 Fibroblast, PBS control, replicate 4 Fibroblast, PBS contro…
GSM9796833 Fibroblast, Strain 48, replicate 4 Fibroblast, Strain 48,
GSM9796834 Fibroblast, Strain 47, replicate 4 Fibroblast, Strain 47,

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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.