CD4 T cell receptor hierarchies are stable and independent of HIV-mediated dysregulation of immune homeostasis

<p>LT-ART and A5248&nbsp;folders contain&nbsp;preprocessed CyTOF files (FCS format) from a 31-marker mass cytometry panel to examine all major PBMC lineages and specifically CD4 and CD8 T cell memory dynamics in people with HIV (PWH) who are durably ART suppressed for an average of 6.7 years (LT-ART, n = 10) and PWH in the first 500 days following ART initiation (A5248, n = 10). The panel also includes markers of activation (HLA-DR, CD38, CCR5), activation/exhaustion (PD-1), proliferation (Ki67), survival (Bcl-2) and long-lived memory (CD127).</p> <p>Preprocessed annotated data objects (A5248_subsample.h5ad, LT-ART_subsample.h5ad) for unsupervised analysis can be accessed using the &#39;read_h5ad&#39; function in Scanpy.</p> <p>CD4_MSI and CD8_MSI folders contain the MSI data for the Gamma fixed-effects regression models.&nbsp;</p> <p>All source code for reproduction of the results can be found in the GitHub repository:&nbsp;<a href="https://github.com/glab-hiv/immune-recovery">https://github.com/glab-hiv/immune-recovery</a></p>