This repo contains code supporting the manuscript "Integrated analysis of immunometabolic interactions in Down syndrome" by Gillenwater et al. (2024)
To download the necessary scripts, clone this repository with:
git clone https://github.com/CostelloLab/ImmunoMetabolicSubtypes/
All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. The demographics and clinical data for ~700 research participants in the HTP study are available on both the Synapse data sharing platform (https://doi.org/10.7303/syn31488784) and the INCLUDE Data Hub (https://portal.includedcc.org/). Whole blood transcriptome data for 400 research participants (26) can be accessed through Synapse (https://doi.org/10.7303/syn31488780), the INCLUDE Data Hub, and Gene Expression Omnibus (GSE190125). Transcriptome data from murine tissues can be accessed through the Gene Expression Omnibus under accession numbers GSE229762 and GSE229737. Targeted plasma proteomics data for inflammatory markers using MSD assays for 470+ research participants (25) can be accessed through Synapse (https://doi.org/10.7303/syn31475487) and the INCLUDE Data Hub. Plasma metabolomics data for 410+ participants can be accessed through Synapse (https://doi.org/10.7303/syn31488782), Metabolomics Workbench (study ID ST002200; http://dev.metabolomicsworkbench.org:22222/data/DRCCMetadata.php?Mode=Study&StudyID=ST002200&Access=UrlT3545), and the INCLUDE Data Hub.