GEO series

Broad spectrum efficacy of BDGR-164 against neurotropic alphaviruses and correlates of protection

GSE255795 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2025/01/06 Platform GPL17021

At a glance

RNA-seq (gene expression) · mouse · 28 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: 28 samples: 7 conditions, mostly with about 4 replicates eachGroups 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: The antiviral BDGR-49 provides protection from lethal, neurotropic Venezuelan equine encephalitis virus intranasal infection in miceJournal of virology · 2025

Summary (written by the submitters)

Infections by the New World alphaviruses, Eastern Equine encephalitis virus (EEEV), Venezuelan Equine encephalitis virus (VEEV), and Western Equine encephalitis virus (WEEV), cause febrile illness that can progress to fatal disease in humans and equids. Currently there are no FDA-approved antivirals for prophylactic or therapeutic treatment of human infection by these viruses.

Read the full summary ↓

To combat these infections, we have developed a novel small molecule, BDGR-164, which has subnanomolar potency against VEEV, EEEV, and WEEV. Using an intranasal route of virus infection in a lethal BALB/c model, prophylactic subcutaneous administration of BDGR-164 conferred 100% (VEEV), 88% (EEEV), and 63% (WEEV) survival. To evaluate the ability of BDGR-164 to reduce viral RNA/antigen, inflammation, and pathogenesis, we used RNASeq and histopathology of whole brain at 4 days post-infection (dpi). Viral RNA levels and antigen were reduced significantly in virus-infected and BDGR-164-treated versus virus-infected, sham-treated mice. Moreover, there was a significant reduction in host immune responses associated with inflammatory signaling, immune cell recruitment, and programmed cell death in virus-infected, BDGR-164 treated mice. Cytokine analyses of sera corroborated the reduction in upregulation of the immune response in virus-infected, BDGR-164 treated mice. Limited antiviral resistance to BDGR-164 was detected in one mouse on 4 dpi at NSP2:Y102C. In conclusion, our studies suggest that BDGR-164 has broad and potent prophylactic efficacy against the neurotropic alphaviruses.

Published in

The antiviral BDGR-49 provides protection from lethal, neurotropic Venezuelan equine encephalitis virus intranasal infection in mice

Williams EP, Xue Y, Vogel P et al. · Journal of virology 2025 · PMID 39936916 · doi:10.1128/jvi.01679-24

This dataset

Open GSE255795 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 GSE255795_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 PRJNA1076535 and SRA study SRP489748. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39936916) ↗

Study design

7 conditions, mostly with about 4 replicates each

PBS, 48 mkd, ×4 VEEV, 0 mkd, ×4 VEEV, 48 mkd, ×4 EEEV, 48 mkd, ×4 EEEV, 0 mkd, ×4 WEEV, 48 mkd, ×4 WEEV, 0 mkd, ×4

Supports a between-group comparison across 28 samples.

How we read this: 7 replicated groups read from 28 sample titles; they account for 28 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

GSM8080222 PBS, 48 mkd, Rep 1 PBS, 48 mkd,
GSM8080223 PBS, 48 mkd, Rep 2 PBS, 48 mkd,
GSM8080224 PBS, 48 mkd, Rep 3 PBS, 48 mkd,
GSM8080225 PBS, 48 mkd, Rep 4 PBS, 48 mkd,
GSM8080226 VEEV, 0 mkd, Rep 1 VEEV, 0 mkd,
GSM8080227 VEEV, 0 mkd, Rep 2 VEEV, 0 mkd,
GSM8080228 VEEV, 0 mkd, Rep 3 VEEV, 0 mkd,
GSM8080229 VEEV, 0 mkd, Rep 4 VEEV, 0 mkd,
GSM8080230 VEEV, 48 mkd, Rep 1 VEEV, 48 mkd,
GSM8080231 VEEV, 48 mkd, Rep 2 VEEV, 48 mkd,
GSM8080232 VEEV, 48 mkd, Rep 3 VEEV, 48 mkd,
GSM8080233 VEEV, 48 mkd, Rep 4 VEEV, 48 mkd,
GSM8080234 EEEV, 48 mkd, Rep 1 EEEV, 48 mkd,
GSM8080235 EEEV, 48 mkd, Rep 2 EEEV, 48 mkd,
GSM8080236 EEEV, 48 mkd, Rep 3 EEEV, 48 mkd,
GSM8080237 EEEV, 48 mkd, Rep 4 EEEV, 48 mkd,
GSM8080238 EEEV, 0 mkd, Rep 1 EEEV, 0 mkd,
GSM8080239 EEEV, 0 mkd, Rep 2 EEEV, 0 mkd,
GSM8080240 EEEV, 0 mkd, Rep 3 EEEV, 0 mkd,
GSM8080241 EEEV, 0 mkd, Rep 4 EEEV, 0 mkd,
GSM8080242 WEEV, 48 mkd, Rep 1 WEEV, 48 mkd,
GSM8080243 WEEV, 48 mkd, Rep 2 WEEV, 48 mkd,
GSM8080244 WEEV, 48 mkd, Rep 3 WEEV, 48 mkd,
GSM8080245 WEEV, 48 mkd, Rep 4 WEEV, 48 mkd,
GSM8080246 WEEV, 0 mkd, Rep 1 WEEV, 0 mkd,
GSM8080247 WEEV, 0 mkd, Rep 2 WEEV, 0 mkd,
GSM8080248 WEEV, 0 mkd, Rep 3 WEEV, 0 mkd,
GSM8080249 WEEV, 0 mkd, Rep 4 WEEV, 0 mkd,

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