GEO series

HIV Transgenic Mouse Monocytes Display Increased In Vivo Migration Across the Blood Brain Barrier Associated with Increased Expression of Genes Associated with Mononuclear Leukocyte Migration

GSE319558 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/03/13 Platform GPL24247

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 × WT, Mouse vs 3 × HIV, Mouse vs 3 × HIV LPS, Mouse vs 2 × WT LPS, MouseGroups 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)

Soon after HIV acquisition, circulating HIV-infected monocytes cross the blood-brain barrier (BBB) and infect resident brain microglia and other susceptible cells, establishing a potential viral reservoir. Despite supressive antiretroviral therapy, these HIV-infected cells mediate a neuroinflammatory process causing HIV-associated neurocognitive deficites (HAND) in at least 20% of people with HIV.

Read the full summary ↓

Continued migration of HIV-infected monocytes into the brain may further exacerbate neuroinflammation and replenish viral reservoirs. To ascertain how HIV infection facilitates monocyte passage across the BBB in vivo, we developed a novel mouse model to quantify circulating monocytes supporting HIV production that migrated into the brain. We demontrate that significantly more monocytes from HIV-transgenic mice, capable of supporting HIV production, crossed the BBB compared to control transgenic mouse monocytes. This difference was particularly pronounced after recipient mice were treated with lipopolysaccharide (LPS). To explore the underlying mechanism, we compared the transcriptomes of HIV transgenic mouse monocytes and control mouse monocytes and identified multiple differentially expressed genes linked to mononuclear leukocyte trafficking, including several associated with monocyte chemotaxis. We also evaluated the effect of substance use in combination with HIV infection on monocyte migration across the BBB into the brain by treating HIV transgenic mice with either morphine or methamphetamine. Short-term exposure to either drug did not significantly alter the migration of HIV-transgenic monocytes across the BBB.

This dataset

Open GSE319558 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 GSE319558_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 PRJNA1423729 and SRA study SRP677117. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × WT, Mouse vs 3 × HIV, Mouse vs 3 × HIV LPS, Mouse vs 2 × WT LPS, Mouse

Supports a between-group comparison across 11 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 11 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

GSM9519793 WT, Mouse 1 WT, Mouse
GSM9519794 WT, Mouse 2 WT, Mouse
GSM9519795 WT, Mouse 3 WT, Mouse
GSM9519796 HIV, Mouse 4 HIV, Mouse
GSM9519797 HIV, Mouse 5 HIV, Mouse
GSM9519798 HIV, Mouse 6 HIV, Mouse
GSM9519799 HIV LPS, Mouse 7 HIV LPS, Mouse
GSM9519800 HIV LPS, Mouse 8 HIV LPS, Mouse
GSM9519801 HIV LPS, Mouse 9 HIV LPS, Mouse
GSM9519802 WT LPS, Mouse 10 WT LPS, Mouse
GSM9519803 WT LPS, Mouse 11 WT LPS, Mouse
GSM9519804 WT LPS Mouse 12

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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.