GEO series
Differential pathogenic and molecular features in neurological infection of SARS-CoV-2 Omicron BA.5.2 and BA.2.75 and Delta
GSE234799
Mus musculus (mouse)
RNA-seq (gene expression)
40 samples
Submitted 2025/04/17
Platform GPL21273
At a glance
RNA-seq (gene expression) · mouse · 40 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
- 40 samples: 8 conditions, mostly with about 5 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
- Differential pathogenic and molecular features in neurological infection of SARS-CoV-2 Omicron BA.5.2 and BA.2.75 and DeltaJournal of medical virology · 2024
Summary (written by the submitters)
The Coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a global threat, exacerbated by the emergence of viral variants. Two variants of SARS-CoV-2, Omicron BA.2.75 and BA.5, led to global infection peaks between May 2022 and May 2023, yet their precise characteristics in pathogenesis are not well understood.
Read the full summary ↓
In this study, we compared these two Omicron sublineages with the previously dominant Delta variant using a human angiotensin-converting enzyme 2 knock-in mouse model. As expected, Delta exhibited higher viral replication in the lung and brain than both Omicron sublineages which induced less severe lung damage and immune activation. In contrast, the Omicron variants especially BA.5.2 showed a propensity for cellular proliferation and developmental pathways. Both Delta and BA.5.2 variants, but not BA.2.75, led to decreased pulmonary lymphocytes, indicating differential adaptive immune response. Neuroinvasiveness was shared with all strains, accompanied by vascular abnormalities, synaptic injury, and loss of astrocytes. However, Immunostaining assays and transcriptomic analysis showed that BA.5.2 displayed stronger immune suppression and neurodegeneration, while BA.2.75 exhibited more similar characteristics to Delta in the cortex. Such differentially infectious features could be partially attributed to the weakened interaction between Omicron Spike protein and host proteomes decoded via co-immunoprecipitation followed by mass spectrometry in neuronal cells. Our present study supports attenuated replication and pathogenicity of Omicron variants but also highlights their newly infectious characteristics in the lung and brain, especially with BA.5.2 demonstrating enhanced immune evasion and neural damage that could exacerbate neurological sequelae.
Published in
Wang E, Yang QJ, Xu XX et al.
· Journal of medical virology 2024
· PMID 38235532
· doi:10.1002/jmv.29357
This dataset
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.
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 GSE234799_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA983250 and SRA study SRP443228. Searching any of these in the dataset finder brings you back here.
Study design
8 conditions, mostly with about 5 replicates each
hACE2 lung, mock, 5dpi, ×5
hACE2 lung, Delta, 5dpi, ×5
hACE2 lung, BA.2.75, 5dpi, ×5
hACE2 lung, BA5, 5dpi, ×5
hACE2 cortex, mock, 5dpi, ×5
hACE2 cortex, Delta, 5dpi, ×5
hACE2 cortex, BA.2.75, 5dpi, ×5
hACE2 cortex, BA5, 5dpi, ×5
Supports a between-group comparison across 40 samples.
How we read this: 8 replicated groups read from 40 sample titles; they account for 40 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
- GSM7474925 hACE2 lung, mock, 5dpi, replicate 1 hACE2 lung, mock, 5dpi,
- GSM7474926 hACE2 lung, mock, 5dpi, replicate 2 hACE2 lung, mock, 5dpi,
- GSM7474927 hACE2 lung, mock, 5dpi, replicate 3 hACE2 lung, mock, 5dpi,
- GSM7474928 hACE2 lung, mock, 5dpi, replicate 4 hACE2 lung, mock, 5dpi,
- GSM7474929 hACE2 lung, mock, 5dpi, replicate 5 hACE2 lung, mock, 5dpi,
- GSM7474930 hACE2 lung, Delta, 5dpi, replicate 1 hACE2 lung, Delta, 5dpi,
- GSM7474931 hACE2 lung, Delta, 5dpi, replicate 2 hACE2 lung, Delta, 5dpi,
- GSM7474932 hACE2 lung, Delta, 5dpi, replicate 3 hACE2 lung, Delta, 5dpi,
- GSM7474933 hACE2 lung, Delta, 5dpi, replicate 4 hACE2 lung, Delta, 5dpi,
- GSM7474934 hACE2 lung, Delta, 5dpi, replicate 5 hACE2 lung, Delta, 5dpi,
- GSM7474935 hACE2 lung, BA.2.75, 5dpi, replicate 1 hACE2 lung, BA.2.75, 5d…
- GSM7474936 hACE2 lung, BA.2.75, 5dpi, replicate 2 hACE2 lung, BA.2.75, 5d…
- GSM7474937 hACE2 lung, BA.2.75, 5dpi, replicate 3 hACE2 lung, BA.2.75, 5d…
- GSM7474938 hACE2 lung, BA.2.75, 5dpi, replicate 4 hACE2 lung, BA.2.75, 5d…
- GSM7474939 hACE2 lung, BA.2.75, 5dpi, replicate 5 hACE2 lung, BA.2.75, 5d…
- GSM7474940 hACE2 lung, BA5, 5dpi, replicate 1 hACE2 lung, BA5, 5dpi,
- GSM7474941 hACE2 lung, BA5, 5dpi, replicate 2 hACE2 lung, BA5, 5dpi,
- GSM7474942 hACE2 lung, BA5, 5dpi, replicate 3 hACE2 lung, BA5, 5dpi,
- GSM7474943 hACE2 lung, BA5, 5dpi, replicate 4 hACE2 lung, BA5, 5dpi,
- GSM7474944 hACE2 lung, BA5, 5dpi, replicate 5 hACE2 lung, BA5, 5dpi,
- GSM7474945 hACE2 cortex, mock, 5dpi, replicate 1 hACE2 cortex, mock, 5dp…
- GSM7474946 hACE2 cortex, mock, 5dpi, replicate 2 hACE2 cortex, mock, 5dp…
- GSM7474947 hACE2 cortex, mock, 5dpi, replicate 3 hACE2 cortex, mock, 5dp…
- GSM7474948 hACE2 cortex, mock, 5dpi, replicate 4 hACE2 cortex, mock, 5dp…
- GSM7474949 hACE2 cortex, mock, 5dpi, replicate 5 hACE2 cortex, mock, 5dp…
- GSM7474950 hACE2 cortex, Delta, 5dpi, replicate 1 hACE2 cortex, Delta, 5d…
- GSM7474951 hACE2 cortex, Delta, 5dpi, replicate 2 hACE2 cortex, Delta, 5d…
- GSM7474952 hACE2 cortex, Delta, 5dpi, replicate 3 hACE2 cortex, Delta, 5d…
- GSM7474953 hACE2 cortex, Delta, 5dpi, replicate 4 hACE2 cortex, Delta, 5d…
- GSM7474954 hACE2 cortex, Delta, 5dpi, replicate 5 hACE2 cortex, Delta, 5d…
- GSM7474955 hACE2 cortex, BA.2.75, 5dpi, replicate 1 hACE2 cortex, BA.2.75, …
- GSM7474956 hACE2 cortex, BA.2.75, 5dpi, replicate 2 hACE2 cortex, BA.2.75, …
- GSM7474957 hACE2 cortex, BA.2.75, 5dpi, replicate 3 hACE2 cortex, BA.2.75, …
- GSM7474958 hACE2 cortex, BA.2.75, 5dpi, replicate 4 hACE2 cortex, BA.2.75, …
- GSM7474959 hACE2 cortex, BA.2.75, 5dpi, replicate 5 hACE2 cortex, BA.2.75, …
- GSM7474960 hACE2 cortex, BA5, 5dpi, replicate 1 hACE2 cortex, BA5, 5dpi,
- GSM7474961 hACE2 cortex, BA5, 5dpi, replicate 2 hACE2 cortex, BA5, 5dpi,
- GSM7474962 hACE2 cortex, BA5, 5dpi, replicate 3 hACE2 cortex, BA5, 5dpi,
- GSM7474963 hACE2 cortex, BA5, 5dpi, replicate 4 hACE2 cortex, BA5, 5dpi,
- GSM7474964 hACE2 cortex, BA5, 5dpi, replicate 5 hACE2 cortex, BA5, 5dpi,
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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.