Toy input dataset for "snrnaseq-step1-preprocessing" code, from Wilson et al. 2025 (https://doi.org/10.1101/2025.02.05.636667)

This is a toy dataset that can be used to run code step #1 from Wilson et al. 2025 (https://doi.org/10.1101/2025.02.05.636667), which performs dataset building and preprocessing of single-nucleus RNA sequencing data (Github: https://github.com/amwilson149/snrnaseq-step1-preprocessing/tree/main). To test the code on this dataset, place these files in the 'data' directory of the code repository, and unzip the compressed files. Then run the script. A description of the study using this code follows: For people with HIV (PWH), substance use disorders (SUDs) are a prominent neurological risk factor, and the impacts of both on dopaminergic pathways are a potential point of deleterious convergence. Here, we profile, at single nucleus resolution, the substantia nigra (SN) transcriptomes of 90 postmortem donors in the context of chronic HIV and opioid/cocaine SUD, including 67 prospectively characterized PWH. We report altered microglial expression for hundreds of pro- and anti-inflammatory regulators attributable to HIV, and separately, to SUD. Stepwise, progressive microglial dysregulation, coupled to altered SN dopaminergic and GABAergic signaling, was associated with SUD/HIV dual diagnosis and further with lack of viral suppression in blood. In virologically suppressed donors, SUD comorbidity was associated with microglial transcriptional changes permissive for HIV infection. We report HIV-related downregulation of monoamine reuptake transporters specifically in dopaminergic neurons regardless of SUD status or viral load, and additional transcriptional signatures consistent with selective vulnerability of SN dopamine neurons.