GEO series

Variant-specific disruption to Notch signaling in PAX6 microphthalmia and aniridia patient-derived hiPSC optic vesicles

GSE288049 Homo sapiens (human) RNA-seq (gene expression) 70 samples Submitted 2025/05/22 Platform GPL20301

At a glance

RNA-seq (gene expression) · human · 70 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: 70 samples: 18 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: Variant-specific disruption to notch signalling in PAX6 microphthalmia and aniridia patient-derived hiPSC optic cup-like organoidsBiochimica et biophysica acta. Molecular basis of disease · 2025

Summary (written by the submitters)

The homeobox-containing transcription factor PAX6 is a key regulator of eye development. Pathogenic heterozygous PAX6 variants lead to variable ocular phenotypes. Missense variants are often associated with milder ocular conditions, although variants in the DNA-binding paired domain which alter target binding lead to severe ocular phenotypes including bilateral microphthalmia, similar to SOX2 anophthalmia syndrome. However, the variant-specific pathway disruption resulting in phenotypic heterogeneity is not well understood.

Published in

Variant-specific disruption to notch signalling in PAX6 microphthalmia and aniridia patient-derived hiPSC optic cup-like organoids

Harding P, Owen N, Eintracht J et al. · Biochimica et biophysica acta. Molecular basis of disease 2025 · PMID 40280197 · doi:10.1016/j.bbadis.2025.167869

This dataset

Open GSE288049 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 GSE288049_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 PRJNA1215937 and SRA study SRP559977. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40280197) ↗

Study design

18 conditions, mostly with about 4 replicates each

AN Clone 2, day 35, ×5 AN Clone 2, day 0, ×4 AN Clone 2, day 20, ×4 PX Clone 1, day 0, ×4 PX Clone 1, day 20, ×4 PX Clone 1, day 35, ×4 PX Clone 2, day 0, ×4 PX Clone 2, day 20, ×4 +10 more

Supports a between-group comparison across 70 samples.

How we read this: 18 replicated groups read from 70 sample titles; they account for 70 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

GSM8757955 AN Clone 1, day 0, replicate 1 AN Clone 1, day 0,
GSM8757956 AN Clone 1, day 0, replicate 2 AN Clone 1, day 0,
GSM8757957 AN Clone 1, day 0, replicate 4 AN Clone 1, day 0,
GSM8757958 AN Clone 1, day 20, replicate 2 AN Clone 1, day 20,
GSM8757959 AN Clone 1, day 20, replicate 3 AN Clone 1, day 20,
GSM8757960 AN Clone 1, day 20, replicate 4 AN Clone 1, day 20,
GSM8757961 AN Clone 1, day 35, replicate 2 AN Clone 1, day 35,
GSM8757962 AN Clone 1, day 35, replicate 3 AN Clone 1, day 35,
GSM8757963 AN Clone 1, day 35, replicate 4 AN Clone 1, day 35,
GSM8757964 AN Clone 2, day 0, replicate 1 AN Clone 2, day 0,
GSM8757965 AN Clone 2, day 0, replicate 2 AN Clone 2, day 0,
GSM8757966 AN Clone 2, day 0, replicate 3 AN Clone 2, day 0,
GSM8757967 AN Clone 2, day 0, replicate 4 AN Clone 2, day 0,
GSM8757968 AN Clone 2, day 20, replicate 1 AN Clone 2, day 20,
GSM8757969 AN Clone 2, day 20, replicate 2 AN Clone 2, day 20,
GSM8757970 AN Clone 2, day 20, replicate 3 AN Clone 2, day 20,
GSM8757971 AN Clone 2, day 20, replicate 4 AN Clone 2, day 20,
GSM8757972 AN Clone 2, day 35, replicate 1 AN Clone 2, day 35,
GSM8757973 AN Clone 2, day 35, replicate 2 AN Clone 2, day 35,
GSM8757974 AN Clone 2, day 35, replicate 3 AN Clone 2, day 35,
GSM8757975 AN Clone 2, day 35, replicate 4 AN Clone 2, day 35,
GSM8757976 AN Clone 2, day 35, replicate 5 AN Clone 2, day 35,
GSM8757977 PX Clone 1, day 0, replicate 1 PX Clone 1, day 0,
GSM8757978 PX Clone 1, day 0, replicate 2 PX Clone 1, day 0,
GSM8757979 PX Clone 1, day 0, replicate 3 PX Clone 1, day 0,
GSM8757980 PX Clone 1, day 0, replicate 4 PX Clone 1, day 0,
GSM8757981 PX Clone 1, day 20, replicate 1 PX Clone 1, day 20,
GSM8757982 PX Clone 1, day 20, replicate 2 PX Clone 1, day 20,
GSM8757983 PX Clone 1, day 20, replicate 3 PX Clone 1, day 20,
GSM8757984 PX Clone 1, day 20, replicate 4 PX Clone 1, day 20,
GSM8757985 PX Clone 1, day 35, replicate 1 PX Clone 1, day 35,
GSM8757986 PX Clone 1, day 35, replicate 2 PX Clone 1, day 35,
GSM8757987 PX Clone 1, day 35, replicate 3 PX Clone 1, day 35,
GSM8757988 PX Clone 1, day 35, replicate 4 PX Clone 1, day 35,
GSM8757989 PX Clone 2, day 0, replicate 1 PX Clone 2, day 0,
GSM8757990 PX Clone 2, day 0, replicate 2 PX Clone 2, day 0,
GSM8757991 PX Clone 2, day 0, replicate 3 PX Clone 2, day 0,
GSM8757992 PX Clone 2, day 0, replicate 4 PX Clone 2, day 0,
GSM8757993 PX Clone 2, day 20, replicate 1 PX Clone 2, day 20,
GSM8757994 PX Clone 2, day 20, replicate 2 PX Clone 2, day 20,

+ 30 more — browse all 70 samples with per-sample file links →

Datasets on a similar topic

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GSE265940 Overexpression of extracellular matrix proteins, increased cell death and reduced cell proliferation contribute to the pathophysiology of microphthalmia across in vitro patient-derived models 48 samples shares patient-derived, microphthalmia
GSE307222 Patient-derived cornea organoids as drug repurposing models for aniridia-associated keratopathy 9 samples shares patient-derived, aniridia
GSE291903 Post-replicative initial expression of the cell fate regulator PAX6 during neuroectoderm formation [RNA-seq 1] 14 samples shares pax6
GSE272034 PAX6-WNK2 axis governs corneal epithelial homeostasis 12 samples shares pax6
GSE291908 Post-replicative initial expression of the cell fate regulator PAX6 during neuroectoderm formation 20 samples shares pax6
GSE291907 Post-replicative initial expression of the cell fate regulator PAX6 during neuroectoderm formation [ATAC-seq] 10 samples shares pax6
GSE307568 Patient-derived organoid – immune cell co-culture platform for therapeutics discovery in high-grade endometrial cancer 189 samples shares patient-derived

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