← BioTransfer GEO Dataset Finder
GEO series

Unraveling the web of nAMD: A transcriptomic analysis of age-related macular degeneration-associated cytokines in primary human retinal endothelial cells.

GSE270418 Homo sapiens (human) Single-cell RNA-seq 48 samples Submitted 2025/12/30 Platform GPL20301
At a glance

Single-cell RNA-seq · human · 48 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
48 samples: 8 conditions, mostly with about 6 replicates eachGroups 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.
Summary (written by the submitters)
Neovascular age-related macular degeneration (nAMD) is a complex, blinding retinal disease underpinned by a dynamic and dysregulated interaction among pathogenic cytokines. The present study investigates the impact of six nAMD-associated cytokines, namely transforming growth factor-beta 1 and 2 (TGF-β1/2), tumour necrosis factor-alpha (TNF-α), thrombin, interleukin-6 (IL-6) and vascular endothelial growth factor (VEGF), on the transcriptome of primary human retinal endothelial cells (HRECs), both individually and as a collective 'cocktail'.
Read the full summary ↓
HRECS were treated for 24 hours before being harvested for bulk RNA-seq. In performing this study, we have described the different transcriptomic signatures of each cytokine in driving nAMD-associated inflammatory, angiogenic and fibrotic pathways when presented in isolation to primary HRECs. Additionally, this study dissects a novel 'cocktail’ effect in the collective group characterised by further differential expression of genes, some of which were not induced by any of the individual cytokines. We explore the translatability of our study as an in vitro model of nAMD in endothelial cells by mapping the identified differential expression patterns to marker gene sets identified in previously performed scRNASeq of nAMD-affected human donor eyes.
This dataset
Open GSE270418 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 GSE270418_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1126598 and SRA study SRP515202. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 conditions, mostly with about 6 replicates each
HREC cells, Control ×6 HREC cells, TGFb1 ×6 HREC cells, TGFB2 ×6 HREC cells, TNFa ×6 HREC cells, Thrombin ×6 HREC cells, IL6 ×6 HREC cells, VEGF ×6 HREC cells, All ×6

Supports a between-group comparison across 48 samples.

How we read this: 8 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.