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Extensive modulation of inflammatory and axonal genes led to robust axon regeneration in severe benzalkonium chloride-injured corneas treated with cord blood-derived biologics

GSE241879 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/09/06 Platform GPL28430

At a glance

RNA-seq (gene expression) · mouse · 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: Mus musculus (mouse)
Samples: 12 samples: 3 × Control vs 3 × Vehicle vs 3 × UCS-treated vs 3 × UCPRP-treatedGroups 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)

Modern ophthalmic solutions contain benzalkonium chloride (BAK), a potent antimicrobial preservative, that chronically damages the ocular apparatus. Umbilical cord blood serum (UCS) and platelet-rich plasma (UCPRP) are promising treatments for BAK-injured corneas. Here, for the first time, the feasibility of using both of these biologics for corneal treatment was demonstrated.

Read the full summary ↓

Using animal studies and RNA-seq analysis, it was validated that severe BAK injury led to the upregulation of innate and adaptive immune responses, which corresponded to morphological and pathological changes in the cornea. When UCS and UCPRP were administered, besides significant corneal recovery, widespread immune pathways downregulation was observed. Subsequent verification of some of the genes involved in two of the most notable KEGG pathways suggested that the amelioration of inflammation was likely due to the reduction of immune cells, the decrease in chemoattractants, as well as the lessening of pro-inflammatory MMPs. Besides that, regulation of several key axonal genes led to robust axon recovery that correlated to nearly restored corneal sensitivity. Thus, these findings demonstrated the viability of cord blood-derived therapeutics for treating sustained, BAK-induced injuries in the cornea and also provided evidence that an optimal level of inflammatory response is crucial for stimulating axon regeneration.

This dataset

Open GSE241879 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 GSE241879_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 PRJNA1010670 and SRA study SRP457469. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × Control vs 3 × Vehicle vs 3 × UCS-treated vs 3 × UCPRP-treated

Supports a case/control comparison: 6 samples read as cases, 6 as controls.

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

GSM7744856 Control_1 Control
GSM7744857 Control_2 Control
GSM7744858 Control_3 Control
GSM7744859 Vehicle_1 Vehicle
GSM7744860 Vehicle_2 Vehicle
GSM7744861 Vehicle_3 Vehicle
GSM7744862 UCS-treated_1 UCS-treated
GSM7744863 UCS-treated_2 UCS-treated
GSM7744864 UCS-treated_3 UCS-treated
GSM7744865 UCPRP-treated_1 UCPRP-treated
GSM7744866 UCPRP-treated_2 UCPRP-treated
GSM7744867 UCPRP-treated_3 UCPRP-treated

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