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Oxidative Stress and Inflammation-Related mRNAs Are Elevated in Serum of a Finnish Wet Age-Related Macular Degeneration Cohort

GSE273435 Homo sapiens (human) RNA-seq (gene expression) 124 samples Submitted 2024/11/15 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 124 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
124 samples: 31 conditions, mostly in duplicateGroups 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
Oxidative Stress and Inflammation-Related mRNAs Are Elevated in Serum of a Finnish Wet AMD CohortInvestigative ophthalmology & visual science · 2024
Summary (written by the submitters)
Purpose: Localized diseases are affected by and affect the systemic environment via blood circulation. In our studies, we explored the differences in different types of circulating serum RNAs between wet age-related macular degeneration (wAMD) patients and controls. Methods: Blood samples were obtained from 60 Finnish wAMD patients and 64 controls.
Read the full summary ↓
After serum preparation and RNA sequencing, the count data was examined for differentially expressed genes (DEGs) and further checked for enriched molecular pathways and ontology terms as well as links to clinical data. Results: In our mRNA study, we found many DEGs and some enriched pathways, including the inflammation and cell survival-associated pathway tumor necrosis factor alpha (TNFA) signaling via nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB). The related DEGs were oxidized low-density lipoprotein receptor 1 (OLR1), salt inducible kinase 1 (SIK1), and coagulation factor III (F3). DEGs from degradative macular and retinal processes were also examined, many of which were also related to cardiovascular disease and maintenance. Additionally, DEG counts were inspected in relation to clinical and anti-vascular endothelial growth factor (anti-VEGF) treatment parameters, and glutamine amidotransferase-like class 1 domain-containing 3A (GATD3A) levels were found to be significantly lower in wAMD patients who had been receiving anti-VEGF treatments compared to those who had not yet received any. Conclusions: Since regulatory factors of mitochondrial function, oxidative stress, and inflammation have a significant role in the pathology of AMD, our mRNA study results may support the presence of interplay between systemic factors and wAMD development and progression.
Published in
Oxidative Stress and Inflammation-Related mRNAs Are Elevated in Serum of a Finnish Wet AMD Cohort
Liukkonen M, Heloterä H, Siintamo L et al. · Investigative ophthalmology & visual science 2024 · PMID 39546296 · doi:10.1167/iovs.65.13.30
This dataset
Open GSE273435 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 GSE273435_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 PRJNA1141914 and SRA study SRP523088. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39546296) ↗
Study design
31 conditions, mostly in duplicate
control patient, female, sampling age 77, ID=C ×6 control patient, female, sampling age 83, ID=C ×4 control patient, female, sampling age 72, ID=C ×4 wAMD patient, female, sampling age 77, ID=A ×3 wAMD patient, female, sampling age 84, ID=A ×3 wAMD patient, female, sampling age 89, ID=A ×3 control patient, female, sampling age 73, ID=C ×3 control patient, female, sampling age 74, ID=C ×3 +69 more

Supports a between-group comparison across 78 samples.

How we read this: 31 replicated groups read from 124 sample titles; they account for 78 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

+ 84 more — browse all 124 samples with per-sample file links →

Datasets on a similar topic

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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.