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Characterization of human monocytic cell line THP-1 associated with human 3D skin models under UVA exposure

GSE261112 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/10/01 Platform GPL24676
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: 3 × THP-1 cells, 2D culture, vs 3 × Macrophages, HSE, vs 3 × Macrophages, UV-treated HSE, vs 3 × Macrophages, UV-treated HSE, M2G,Groups 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
Characterization of macrophages associated with human skin models exposed to UV radiationCommunications biology · 2024
Summary (written by the submitters)
Tissue resident macrophages play important roles in tissue homeostasis and acute response to external stimuli. Human skin equivalents (HSEs) incorporating human monocytic cell line THP-1, were fabricated to generate immunocompetent human skin models. These HSEs were used to investigate the influence of the skin microenvironment and UVA exposure on the phenotypes of macrophages.
Read the full summary ↓
THP-1 in HSEs exhibited mixed M1 and M2 macrophage phenotypes. Transcriptomic analysis demonstrated that THP-1 in HSEs enriched extracellular matrix interaction while downregulated a DNA replication hallmark. Upon UVA exposure, immunocompetent HSEs exhibited epidermal distortion and increased DNA double-strand breaks (DSB). THP-1 isolated from UVA-exposed HSEs revealed significant upregulation of genes associated with oxidative stress, antioxidant regulation, inflammatory and UV response. A photoprotective agent, mycosporine-2-glycine (M2G), derived from cyanobacteria was applied on to immunocompetent HSEs and the responses of THP-1 cell line was investigated after UVA exposure. The result showed that UVA-induced DSB was significantly lower in M2G-treated HSEs. In addition, the inflammatory and UV response hallmarks were downregulated while the oxidative phosphorylation hallmark was upregulated in THP-1 from M2G-treated UVA exposed HSEs. Taken together, this study provides an immunocompetent 3D skin model that can be used to interrogate responses of skin resident innate immune cells to microenvironment and external stimuli such as UVA irradiation.
Published in
Characterization of macrophages associated with human skin models exposed to UV radiation
Phuphanitcharoenkun S, Louis F, Sowa Y et al. · Communications biology 2024 · PMID 39379484 · doi:10.1038/s42003-024-06975-z
This dataset
Open GSE261112 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 GSE261112_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 PRJNA1085308 and SRA study SRP494004. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39379484) ↗
Study design
3 × THP-1 cells, 2D culture, vs 3 × Macrophages, HSE, vs 3 × Macrophages, UV-treated HSE, vs 3 × Macrophages, UV-treated HSE, M2G,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
Datasets on a similar topic

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