CD4 T cell receptor hierarchies are stable and independent of HIV-mediated dysregulation of immune homeostasis
Description
LT-ART and A5248 folders contain 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).
Preprocessed annotated data objects (A5248_subsample.h5ad, LT-ART_subsample.h5ad) for unsupervised analysis can be accessed using the 'read_h5ad' function in Scanpy.
CD4_MSI and CD8_MSI folders contain the MSI data for the Gamma fixed-effects regression models.
All source code for reproduction of the results can be found in the GitHub repository: https://github.com/glab-hiv/immune-recovery
Files
A5248.zip
Files
(6.0 GB)
| Name | Size | Download all |
|---|---|---|
|
md5:6d80d022967e953a01b8802beb1b5a38
|
4.4 GB | Preview Download |
|
md5:3f6ea481c47b4a3f4b35e64aa2cbdc20
|
45.1 MB | Download |
|
md5:206917310f950b929a51f1b4de04117c
|
38.6 kB | Preview Download |
|
md5:dbc214fd23812e257421a5758fe05ad4
|
38.5 kB | Preview Download |
|
md5:3752dbc4572829da13a67d5c0e0f738a
|
1.5 GB | Preview Download |
|
md5:7c069f0279b89c139b162d5da6f6b76a
|
12.8 MB | Download |