This repository has the data for Simonich et al (2025), a study on RSV evolution from the Bloom lab.
Study done by Cassie Simonich and Teagan McMahon starting in 2024. This study validates a pseudovirus based neutralization assay developed by the authors and also looks at how well mAbs and human serum retain their neutralization as RSV evolves over time.
- ./01_data/
- ./frac_infect/: Processed data used for analysis.
- ./combined_frac_infect/: combined files based on experiment_rep for use in plotting/summary tables
- ./raw_plate_reader/: Raw data, not read into the notebooks.
- ./maps/: includes .csv files of the plate maps used to calculate fraction infectivity from .xlsx files
- ./PlateLayouts/: includes .csv files of the plate layouts used to calculate fraction infectivity from .xlsx files
- ./other/: includes .csv files for plotting of other (non fraction infectivity) data type, mainly titer data. Also includes fraction infectivities for the 293T vs 293T TIM1 test
- ./02_notebooks/: Jupyter notebooks for data processing and visualization.
- ./03_output/
- ./plots/: Saved plots from the notebooks.
- ./processed_data/: Data files processed in the notebooks.
- ./summary_tables/: manually reformated data useful in the paper (ex. summary IC50/NT50, antibody sequences)
- ./04_plasmid_maps/:
- includes all plasmid maps (.gb) used in the study
- ./auspice/:
- This directory includes JSON trees for RSV A and B F proteins, named so that they display via Nextstrain Community Builds at https://nextstrain.org/community/jbloomlab/RSV-evolution-neut@main/RSV-A-F and https://nextstrain.org/community/jbloomlab/RSV-evolution-neut@main/RSV-B-F. These trees were created by running the NextStrain RSV build at https://github.com/nextstrain/rsv but removing the step to subsample sequences for the F gene builds, on May-9-2024.
- at github page with properly rendered figures can be found here