GEO series

Stage-specific phenotypic and transcriptional alterations in HaCaT keratinocytes exposed to acute and chronic blue light

GSE289880 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/04/07 Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 12 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: 12 samples: 12 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: Stage-specific phenotypic and transcriptional alterations in HaCaT keratinocytes exposed to acute and chronic blue lightPhotochemistry and photobiology · 2025

Summary (written by the submitters)

Despite evidence that visible light (VL) has similar effects on human skin as those of UVA, VL is often viewed as harmless. High SPF sunscreen prevents erythema but can lead to overexposure to UVA and VL, with unknown consequences. To explore the impact of chronic blue light exposure, we irradiated (50 J/cm², λ= 408 nm, three times a week) human immortalized keratinocytes under acute (3 irradiations), intermediate (14 irradiations), and chronic (42 irradiations) blue-light exposure, monitoring phenotypic and gene expression changes.

Read the full summary ↓

Chronically exposed keratinocytes exhibit increased nuclei area, chromatin alterations, higher proliferation, and apoptosis resistance, mirroring the consequences of chronic UVA exposure. While acute exposure upregulated keratinization and downregulated tissue repair and apoptosis genes, chronically exposed cells had upregulated genes involved with energy metabolism and oxidative phosphorylation and downregulated genes were enriched for immune and inflammatory responses. Specific transcription factors were identified in both the acute and chronic stages, some of which have been associated with UVB exposure. In the acute stage, IRF1, EGR1, ELF3, and FOSL1 were noted, while in the chronic stage, CENPX, SRF, CEBPB, and KLF4 were identified. We identified some changes in chronically irradiated keratinocytes similar to the malignant transformation, emphasizing the need for further research on the long-term impacts of blue light exposure on human skin.

Published in

Stage-specific phenotypic and transcriptional alterations in HaCaT keratinocytes exposed to acute and chronic blue light

Tonolli PN, Marie SKN, Oba-Shinjo SM et al. · Photochemistry and photobiology 2025 · PMID 40191980 · doi:10.1111/php.14095

This dataset

Open GSE289880 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 GSE289880_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 PRJNA1225239 and SRA study SRP564676. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40191980) ↗

Study design

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

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 12 sample titles: 12 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

GSM8800801 darkX3a
GSM8800802 darkX3b
GSM8800803 blueX3a
GSM8800804 blueX3b
GSM8800805 darkX14a
GSM8800806 darkX14b
GSM8800807 blueX14a
GSM8800808 blueX14b
GSM8800809 darkX42a
GSM8800810 darkX42b
GSM8800811 blueX42a
GSM8800812 blueX42b

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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.