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Development of an antisense oligonucleotide targeting EFEMP1 in models relevant to macular degeneration

GSE289976 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2026/08/03 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 15 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
15 samples: 15 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.
Summary (written by the submitters)
Antisense oligonucleotides (ASOs) are RNA targeting therapies with substantial potential for the medical treatment of genetically defined inherited ocular conditions and beyond. The eye is, in principle an ideal model for ASO therapeutic development due to the ease of administration and potential limited dosing frequency due to ASO durability.
Read the full summary ↓
Autosomal dominant drusen (ADD) is an inherited retinal dystrophy characterized by early onset formation of numerous drusen with subsequent choroidal neovascularization (CNV). ADD is caused by a mutation in the epidermal growth factor-containing fibrillin-like extracellular matrix protein 1 (EFEMP1). EFEMP1R345W is expressed at high levels in the retinal pigmented epithelium (RPE) and accumulates both intracellularly and in the extracellular matrix (ECM) of the RPE during ADD. Furthermore, EFEMP1 has been reported to be significantly upregulated in serum and RPE/choroid during age-related macular degeneration (AMD) yet the consequence of EFEMP1 overexpression has not been fully elucidated. Here, we report the development of a biallelic EFEMP1 targeted ASO that has shown robust EFEMP1 knockdown and modulation of disease relevant factors in induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE), human microvascular retinal endothelial cells (HMREC), ex vivo human choroidal explants and in vivo mouse models. We further demonstrate that EFEMP1 is upregulated at the protein level during AMD. Herein, we report that EFEMP1 knockdown reduces complement factor 3 (C3) levels, a current target for AMD, and significantly reduces proliferation and migration in HMREC and a human choroidal explant sprouting. In summary, we propose a EFEMP1 targeted ASO as a therapeutic modality for DHRD and AMD.
This dataset
Open GSE289976 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 GSE289976_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 PRJNA1225679 and SRA study SRP564991. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
15 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 15 sample titles: 15 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
Datasets on a similar topic

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