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Transcriptome changes driving multiple regulatory pathways involved in TGF-β-induced Anterior Subcapsular Cataract

GSE336537 Mus musculus (mouse) RNA-seq (gene expression) 10 samples Submitted 2026/06/25 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 10 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
Mus musculus (mouse)
Samples
10 samples: 4 × TGFB1-overexpressing lens epithelium (OVE918) vs 3 × Wild-type lens epithelium vs 3 × TGFB1-overexpressing lens epithelium (OVE853)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)
Transforming Growth Factor-beta (TGF-β) promotes lens epithelial-mesenchymal tran-sition (EMT) and fibrosis, contributing to anterior subcapsular cataract (ASC) formation. Transgenic mice overexpressing TGF-β1 in lens have been studied for over three decades, and yet the impact of active TGF-β1-overexpression on the lens epithelial transcriptome is undefined.
Read the full summary ↓
We have addressed this knowledge gap by examining the gene expression landscape of these unique lens epithelia. High-throughput RNA-sequencing was per-formed on isolated lens epithelia from three-week-old TGF-β1-overexpression trans-genic mice from two independent lines, OVE853 and OVE918, and wild-type mice. Downstream analyses included comparisons with lens datasets (e.g., cataract-surgery model) and investigations using various resources/tools (e.g., Gene Ontology, CompBio, iSyTE). Compared to wild-type murine lens epithelia, 384 differentially expressed genes (DEGs) were commonly identified in lens of both transgenic lines. Candidates involved in EMT, inflammatory response, extracellular matrix organization, and mecha-no-sensation were elevated, while those involved in lipid metabolism, Wnt-suppression, Bmp- and Notch-activation were reduced. Comparative analyses with temporal tran-scriptomes on a mouse cataract-surgery model identified overlapping pathological pathways, and some elevated genes, for example endoplasmic reticulum stress genes, were in agreement with human ASC data. A major discovery was the identification of several novel TGF-β1-targets. All our data is made user-friendly accessible through iSyTE.
This dataset
Open GSE336537 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 GSE336537_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 PRJNA1481952 and SRA study SRP712520. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × TGFB1-overexpressing lens epithelium (OVE918) vs 3 × Wild-type lens epithelium vs 3 × TGFB1-overexpressing lens epithelium (OVE853)

Supports a case/control comparison: 7 samples read as cases, 3 as controls.

How we read this: 3 replicated groups read from 10 sample titles; they account for 10 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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