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Genomic characterization of sub-populations in human pluripotent stem cell-derived retinal progenitor cells that drive retinal layer structure

GSE297722 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2026/03/05 Platform GPL33758
At a glance

Single-cell RNA-seq · human · 12 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
12 samples: 3 × NL-spheroids on PS-Day vs 3 × WL-spheroids on PS-Day vs 3 × P-spheroids on PS-DayGroups 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
Genomic characterization of sub-populations in human pluripotent stem cell-derived retinal progenitor cells driving retinal laminationStem cell reports · 2026
Summary (written by the submitters)
The mechanisms of layer formation of retinal spheroids were investigated using Rax::GFP-positive retinal progenitor cells (RPCs) obtained from human embryonic stem cell-derived retinal organoids. Single-cell RNA sequencing revealed that well-layered spheroids exhibited a transient activation of canonical WNT2B–FZD7 signaling followed by a temporary expression of non-canonical WNT5A, processes associated with the formation of organized retinal layers.
Read the full summary ↓
Despite structural differences in vitro, both non-layered and well-layered retinal spheroids of differentiation day 60 successfully developed into each cone and rod subtypes of photoreceptors and established synaptic connections with host bipolar cells after transplantation in retinal degeneration model rats, resulting in light-evoked functional recovery.　Additionally, part of the presumable RPCs differentiated into non-retinal lineages, including ciliary marginal zone-like, retinal pigment epithelium-, and spinal cord-like tissues in vitro, reflecting the developmental plasticity of RAX-positive cells. These findings suggest that canonical and non-canonical WNT signaling pathways sequentially orchestrate early retinal morphogenesis, while environmental factors within the host retina strongly drive the alignment and functional integration of graft photoreceptors.
Published in
Genomic characterization of sub-populations in human pluripotent stem cell-derived retinal progenitor cells driving retinal lamination
Iwama Y, Masuda T, Yoshimura M et al. · Stem cell reports 2026 · PMID 41791386 · doi:10.1016/j.stemcr.2026.102831
This dataset
Open GSE297722 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 GSE297722_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 PRJNA1265961 and SRA study SRP587455. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41791386) ↗
Study design
3 × NL-spheroids on PS-Day vs 3 × WL-spheroids on PS-Day vs 3 × P-spheroids on PS-Day

Supports a between-group comparison across 9 samples.

How we read this: 3 replicated groups read from 12 sample titles; they account for 9 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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