GEO series

IKKα signaling in the nucleus or cytoplasm of keratinocytes leads to opposite skin phenotypes.

GSE239533 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2024/11/14 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 18 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: Mus musculus (mouse)
Samples: 18 samples: 13 distinct titles, 1 of them repeatedGroups 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: Nuclear versus cytoplasmic IKKα signaling in keratinocytes leads to opposite skin phenotypes and inflammatory responses, and a different predisposition to cancerOncogene · 2025

Summary (written by the submitters)

The skin exerts essential roles for the organism survival, such as environmental barrier and immune functions. IKKα is known as an essential protein for skin homeostasis. However, the functions performed by IKKα in the skin and the mechanisms it employs are largely unknown, leading to contradictory interpretations and results regarding the consequences of its deregulation in pathologies such as non-melanoma skin cancer (NMSC).

Read the full summary ↓

Here, using our previously generated transgenic mouse models which express IKKα in the cytoplasm (C-IKKα mice) or in the nucleus (N-IKKα mice) of basal keratinocytes, we demonstrate that at each subcellular localization, IKKα distinctly regulates signaling pathways important for maintaining the balance between keratinocyte proliferation and differentiation, as well as the inflammatory response of the skin. As a result, N-IKKα mice show an atrophic epidermis with exacerbated terminal differentiation, reminiscent of alterations observed in patients with ichthyosis. Conversely, C-IKKα mice display a hyperplastic epidermis with impaired epidermal differentiation and pustular inflammation, resembling patients with pustular psoriasis. Interestingly, C-IKKα keratinocytes are almost devoid of nuclear IKKα due to endogenous IKKα downregulation. However, these changes in the skin of C-IKKα mice do not lead to the development of squamous cell carcinomas (SCCs), unlike N-IKKα mice, which develop spontaneous SCCs.

Published in

Nuclear versus cytoplasmic IKKα signaling in keratinocytes leads to opposite skin phenotypes and inflammatory responses, and a different predisposition to cancer

García-García VA, Alameda JP, Fernández-Aceñero MJ et al. · Oncogene 2025 · PMID 39511409 · doi:10.1038/s41388-024-03203-0

This dataset

Open GSE239533 in finder → Find more mouse 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 GSE239533_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 PRJNA999660 and SRA study SRP451985. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39511409) ↗

Study design

13 distinct titles, 1 of them repeated

Wild type mouse, WT ×6

How we read this: Read from 18 sample titles: 13 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

GSM7666990 Wild type mouse, WT1
GSM7666991 Wild type mouse, WT2
GSM7666992 Wild type mouse, WT3
GSM7666993 Wild type mouse, WT4
GSM7666994 Wild type mouse, WT5
GSM7666995 Wild type mouse, WT6
GSM7666996 Transgenic N-IKKα mouse, 7N
GSM7666997 Transgenic N-IKKα mouse, 8N
GSM7666998 Transgenic N-IKKα mouse, 9N
GSM7666999 Transgenic N-IKKα mouse, 10N
GSM7667000 Transgenic N-IKKα mouse, 11N
GSM7667001 Transgenic N-IKKα mouse, 12N
GSM7667002 Transgenic C-IKKα mouse, 13C
GSM7667003 Transgenic C-IKKα mouse, 14C
GSM7667004 Transgenic C-IKKα mouse, 15C
GSM7667005 Transgenic C-IKKα mouse, 16C
GSM7667006 Transgenic C-IKKα mouse, 17C
GSM7667007 Transgenic C-IKKα mouse, 18C

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