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Epithelial MAPK Signaling Directs Endothelial NRF2 Signaling and IL-8 Secretion in the Alveolar Capillary Region

GSE229544 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2024/12/01 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
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
Epithelial MAPK signaling directs endothelial NRF2 signaling and IL-8 secretion in a tri-culture model of the alveolar-microvascular interface following diesel exhaust particulate (DEP) exposureParticle and fibre toxicology · 2024
Summary (written by the submitters)
Particulate matter 2.5 (PM2.5) deposition in the lung’s alveolar capillary region (ACR) is significantly associated with respiratory disease development, yet the underlying molecular mechanisms are not completely understood. Adverse responses that promote respiratory disease development involve orchestrated, intercellular signaling between multiple cell types within the ACR.
Read the full summary ↓
Our goal was to use an organotypic, in vitro model of the ACR to investigate if alveolar epithelial PM2.5 exposure induces exposure responses in alveolar epithelial cells and in underlying microvascular endothelial cells in the ACR. Our findings demonstrate that alveolar epithelial PM2.5 exposure induces robust transcriptional responses in the microvascular endothelial cells within the ACR. We show that the underlying microvascular endothelial cells develop redox dysfunction and increase proinflammatory cytokine secretion, two exposure responses commonly associated with respiratory disease development. Moreover, we identified intercellular signaling mechanisms between the alveolar epithelium and microvascular endothelium that modulate these adverse endothelial exposure responses. Our findings illustrate a new mechanism of intercellular communication between cells of the ACR that significantly improves our understanding of respiratory disease development following pulmonary exposure to inhaled materials.
Published in
Epithelial MAPK signaling directs endothelial NRF2 signaling and IL-8 secretion in a tri-culture model of the alveolar-microvascular interface following diesel exhaust particulate (DEP) exposure
Vitucci ECM, Simmons AE, Martin EM et al. · Particle and fibre toxicology 2024 · PMID 38468337 · doi:10.1186/s12989-024-00576-8
This dataset
Open GSE229544 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 GSE229544_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 PRJNA954854 and SRA study SRP432297. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38468337) ↗
Samples in this study

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