Science Advances

This dataset contains the raw data supporting all main and supplementary figures used in the manuscript "Mucosal immunization with ChAd-SARS-CoV-2-S prevents sequential transmission of SARS-CoV-2 to unvaccinated hamsters" published in Science Advances. The data contains viral and antibody titers from hamsters not-vaccinated, mucosally vaccinated, or systemically vaccinated and then exposed to SARS-CoV-2 positive hamsters.

SARS-CoV-2’s transmission bottleneck remains poorly characterized, in part due to a lack of quantitative measurement tools. To address this, we adapted a SARS-CoV-2 reverse genetics system to generate a pool of >200 isogenic SARS-CoV-2 viruses harboring specific 6-nucleotide barcodes inserted in ORF10, a non-translated ORF. We directly inoculated donor Syrian hamsters intranasally with this barcoded virus pool and exposed a paired naïve contact hamster to each donor. Following exposure, the nasal turbinates, trachea, and lungs were collected, viral titers were measured, and the number of barcodes in each tissue were enumerated to quantify the transmission bottleneck. The duration and route (airborne, direct contact, and fomite) of exposure were varied to assess their impact on the transmission bottleneck. Primarily, the dataset contains (1) fastq files from next-generation sequencing of a small amplicon that contains the barcode of our barcoded viruses and (2) associated count matrices showing how many of each barcode are present in each sample. Secondarily, RT-qPCR results measuring viral titers in various respiratory tissues are also included.

While contemporary work has begun to appreciate the functional diversity of ventral pallidum (VP), the molecular heterogeneity underlying its functional diversity remains incompletely understood. Here, we used snRNA-seq to define the transcriptional taxonomy of distinct cell types in the VP in mice (Mus musculus), macaques (Macaca mulatta) and baboons (Papio anubis). The dataset contains the snRNA-seq data and analysis meta data that are required to reproduce the independent snRNA-seq analysis for each species and integrated analysis, related to Fig 1, 4 and 5 of the manuscript.

These data correspond to the results reported in J. Borge-Holthoefer, Nicola Perra, Bruno Gonçalves, Sandra González-Bailón, Alex Arenas, Yamir Moreno and Alessandro Vespignani. The dynamic of information-driven coordination phenomena: a transfer entropy analysis. Science Advances 2(4) e1501158 (2016) doi: 10.1126/sciadv.1501158 (open access) Check the readme.txt file in the tar.gz for further information.