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Overexpression of extracellular matrix proteins, increased cell death and reduced cell proliferation contribute to the pathophysiology of microphthalmia across in vitro patient-derived models

GSE265940 Homo sapiens (human) RNA-seq (gene expression) 48 samples Submitted 2024/06/04 Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 48 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
48 samples: 12 conditions, mostly with about 4 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.
Paper
Disruption of common ocular developmental pathways in patient-derived optic vesicle models of microphthalmiaStem cell reports · 2024
Summary (written by the submitters)
Genetic perturbations influencing early eye development can result in microphthalmia, anophthalmia and coloboma (MAC). Over 100 genes are associated with MAC, but little is known about common disease mechanisms. In this study, we generated induced pluripotent stem cell (iPSC) derived optic vesicles (OVs) from two unrelated microphthalmia patients and healthy controls.
Read the full summary ↓
At day 20, 35 and 50 microphthalmia patient OV diameters were significantly smaller, recapitulating the ‘small eye’ phenotype. RNA-seq analysis revealed upregulation of apoptosis-initiating and extracellular matrix (ECM) genes at day 20 and 35. Western blot and immunohistochemistry revealed increased expression of lumican, nidogen and collagen type IV, suggesting ECM overproduction. Increased apoptosis was observed in microphthalmia OVs with reduced pH3+ cells confirming decreased cell proliferation at day 35. Pharmacological inhibition of caspase-8 activity with Z-IETD-FMK decreased apoptosis in one patient model, highlighting a potential therapeutic approach. These data reveal shared pathophysiological mechanisms contributing to a microphthalmia phenotype.
Published in
Disruption of common ocular developmental pathways in patient-derived optic vesicle models of microphthalmia
Eintracht J, Owen N, Harding P et al. · Stem cell reports 2024 · PMID 38821055 · doi:10.1016/j.stemcr.2024.05.001
This dataset
Open GSE265940 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 GSE265940_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 PRJNA1105010 and SRA study SRP504205. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38821055) ↗
Study design
12 conditions, mostly with about 4 replicates each
retinal organoid, control, day 20, clone 1, ×4 retinal organoid, control, day 20, clone 2, ×4 retinal organoid, control, day 35, clone 1, ×4 retinal organoid, control, day 35, clone 2, ×4 retinal organoid, PX, day 20, clone 1, ×4 retinal organoid, PX, day 20, clone 2, ×4 retinal organoid, PX, day 35, clone 1, ×4 retinal organoid, PX, day 35, clone 2, ×4 +4 more

Supports a between-group comparison across 48 samples.

How we read this: 12 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

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