GEO series

The effect of nanoseond laser on murine retinal pigment epithelial cells

GSE287768 Mus musculus (mouse) Single-cell RNA-seq 11 samples Submitted 2025/03/26 Platform GPL19057

At a glance

Single-cell RNA-seq · mouse · 11 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: Mus musculus (mouse)
Samples: 11 samples: 6 × C vs 5 × LGroups 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: Nanosecond laser induces proliferation and improved cellular health within the retinal pigment epitheliumFrontiers in medicine · 2025

Summary (written by the submitters)

Ophthalmic laser treatment using short pulse lasers has shown promise as a treatment for certain eye diseases such as Age related macular degeeneration. In this study we treated C57BL/6J mice at 9 months of age with 10 laser spots delivered by the 2RT nanosecond laser. Animal were allowed to recover and were aged a further 3 months (12 months old) before retinal pigment epithelial (RPE) cells were isolated.

Read the full summary ↓

Totsal RNA samples from laser-treated and control animals were isolated and preamplified using the SMARTSeq v4 low RNA input kit. After library preparation a 50bp single end read was performed at a depth of 19-34 million reads per sample using the Illumina HiSeq. Constructs were mapped to the murine genome and differential expression calculated between the laser-treated and control groups. underwent RNAseq o

Published in

Nanosecond laser induces proliferation and improved cellular health within the retinal pigment epithelium

Jobling AI, Findlay Q, Greferath U et al. · Frontiers in medicine 2025 · PMID 40098930 · doi:10.3389/fmed.2025.1516900

This dataset

Open GSE287768 in finder → Find more mouse 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 GSE287768_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 PRJNA1214589 and SRA study SRP560487. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40098930) ↗

Study design

6 × C vs 5 × L

Supports a between-group comparison across 11 samples.

How we read this: 2 replicated groups read from 11 sample titles; they account for 11 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

GSM8751049 C1 C
GSM8751050 C2 C
GSM8751051 C3 C
GSM8751052 C4 C
GSM8751053 C5 C
GSM8751054 C6 C
GSM8751055 L1 L
GSM8751056 L2 L
GSM8751057 L3 L
GSM8751058 L4 L
GSM8751059 L5 L

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