Title: HR-VILAGE-3K3M: A Comprehensive Human Respiratory Viral Immunization Longitudinal Gene Expression Dataset for Systems Immunity

Abstract:

While respiratory viral infections represent a significant global health challenge, the specific cellular immune pathways responsible for both protective immunity and disease pathology are not yet fully understood. Although natural infection studies often suffer from the absence of pre-exposure baselines and inconsistent timing in sample collection, controlled inoculation and vaccination trials yield highly structured longitudinal transcriptomic data. Despite this, such datasets are currently fragmented across various repositories and subjected to disparate processing methods, which impedes integrative research and AI-driven analysis.

To overcome these obstacles, we have introduced the Human Respiratory Viral Immunization LonginAl Gene Expression (HR-VILAGE-3K3M) repository. This AI-optimized resource consolidates bulk and single-cell transcriptomic profiles derived from 3,178 participants drawn from 66 distinct studies. The collection encompasses data from vaccination, inoculation, and mixed exposure scenarios, utilizing samples obtained from blood and nasal swabs sourced from public databases such as GEO, ImmPort, and ArrayExpress.

Our curation process involved harmonizing subject-level metadata, standardizing outcome metrics, and implementing a unified preprocessing pipeline accompanied by stringent quality control measures. Additionally, we present benchmark analyses to demonstrate the dataset’s practical applications. As one of the most extensive longitudinal transcriptomic resources dedicated to human respiratory viral immunization, HR-VILAGE-3K3M facilitates reproducible and scalable investigations, thereby accelerating advancements in vaccine development and antiviral strategies. This resource is instrumental in uncovering novel biomarkers, elucidating immune mechanisms, and driving methodological innovation.

Source: arXiv Generated at: 2026-06-02 00:00:00 UTC