GEO series

Axonopathy precedes cell death in ocular damage mediated by blast exposure

GSE274793 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2024/08/14 Platform GPL21103

At a glance

RNA-seq (gene expression) · mouse · 24 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: 24 samples: 6 × 8D_Treated vs 6 × 8D_Control vs 6 × 5W_Control vs 6 × 5W_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.
Paper: Axonopathy precedes cell death in ocular damage mediated by blast exposureScientific reports · 2021

Summary (written by the submitters)

Traumatic brain injuries (TBI) of varied types are common across all populations and can cause visual problems. For military personnel in combat settings, injuries from blast exposures (bTBI) are prevalent and arise from a myriad of different situations. To model these diverse conditions, we are one of several groups modeling bTBI using mice in varying ways.

Read the full summary ↓

Here, we report a refined analysis of retinal ganglion cell (RGC) damage in male C57BL/6J mice exposed to a blast-wave in an enclosed chamber. Ganglion cell layer thickness, RGC density (BRN3A and RBPMS immunoreactivity), cellular density of ganglion cell layer (hematoxylin and eosin staining), and axon numbers (paraphenylenediamine staining) were quantified at timepoints ranging from 1 to 17-weeks. RNA sequencing was performed at 1-week and 5-weeks post-injury. Earliest indices of damage, evident by 1-week post-injury, are a loss of RGC marker expression, damage to RGC axons, and increase in glial markers expression. Blast exposure caused a loss of RGC somas and axons-with greatest loss occurring by 5-weeks post-injury. While indices of glial involvement are prominent early, they quickly subside as RGCs are lost. The finding that axonopathy precedes soma loss resembles pathology observed in mouse models of glaucoma, suggesting similar mechanisms.

Published in

Axonopathy precedes cell death in ocular damage mediated by blast exposure

Boehme NA, Hedberg-Buenz A, Tatro N et al. · Scientific reports 2021 · PMID 34083587 · doi:10.1038/s41598-021-90412-2

This dataset

Open GSE274793 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 GSE274793_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 PRJNA1148067 and SRA study SRP526312. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 34083587) ↗

Study design

6 × 8D_Treated vs 6 × 8D_Control vs 6 × 5W_Control vs 6 × 5W_Treated

Supports a case/control comparison: 12 samples read as cases, 12 as controls.

How we read this: 4 replicated groups read from 24 sample titles; they account for 24 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

GSM8458000 8D_Treated_1 8D_Treated
GSM8458001 8D_Treated_2 8D_Treated
GSM8458002 8D_Control_1 8D_Control
GSM8458003 8D_Treated_3 8D_Treated
GSM8458004 8D_Treated_4 8D_Treated
GSM8458005 8D_Control_2 8D_Control
GSM8458006 8D_Control_3 8D_Control
GSM8458007 8D_Treated_5 8D_Treated
GSM8458008 8D_Control_4 8D_Control
GSM8458009 8D_Treated_6 8D_Treated
GSM8458010 8D_Control_5 8D_Control
GSM8458011 8D_Control_6 8D_Control
GSM8458012 5W_Control_1 5W_Control
GSM8458013 5W_Control_2 5W_Control
GSM8458014 5W_Treated_1 5W_Treated
GSM8458015 5W_Treated_2 5W_Treated
GSM8458016 5W_Treated_3 5W_Treated
GSM8458017 5W_Control_3 5W_Control
GSM8458018 5W_Treated_4 5W_Treated
GSM8458019 5W_Treated_5 5W_Treated
GSM8458020 5W_Treated_6 5W_Treated
GSM8458021 5W_Control_4 5W_Control
GSM8458022 5W_Control_5 5W_Control
GSM8458023 5W_Control_6 5W_Control

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.