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Elucidating the molecular mechanisms underlying CRB1-related Leber congenital amaurosis (LCA)

GSE235778 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/06/01 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 12 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
12 samples: 3 × Wildtype control 19, day 35, vs 3 × Wildtype control 35, day 35, vs 3 × CRB1 clone C3, day 35, vs 3 × CRB1 clone C4, day 35,Groups 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)
Patients with genetic mutations in the CRB1 gene have varied clinical features and levels of disease severity ranging from Leber congenital amaurosis (LCA), early onset retinal dystrophy (EORD) to retinitis pigmentosa (RP). The relationship between genetic mutation and clinical presentation is not well understood. Our lab have characterised two disease models of CRB1 (Owen et al 2023); zebrafish and patient grown stem cell derived early retinas.
Read the full summary ↓
Investigation reveals lack of the CRB1 protein prevents the retina from developing into a mature state with precise defined cell types, instead it is locked in an early stage of development with lots of cells dividing. To futher understand the underlying molecular mechanisms causing the CRB1 phenotype we have carried out transcriptome analysis of iPSC derived 3D retinal organoids at day 35.
This dataset
Open GSE235778 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 GSE235778_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 PRJNA987610 and SRA study SRP445976. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × Wildtype control 19, day 35, vs 3 × Wildtype control 35, day 35, vs 3 × CRB1 clone C3, day 35, vs 3 × CRB1 clone C4, day 35,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
Datasets on a similar topic

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