Repository for reproducing analyses related to HHV-6 reactivation in (CAR) T cells manuscript:
Lareau et al. 2023 "Latent human herpesvirus 6 is reactivated in CAR T cells" Nature. DOI: 10.1038/s41586-023-06704-2
Our .fastq files are made available on the Gene Expression Omnibus.
- This repository contains files to reproduce Serratus screening analyses for all viruses (via ViralZone) known to infect humans (see panels b,c). Note: due to the large number of
.softfiles annotating the GSM samples, it made sense to make this a separate repository. - Code to reproduce the followup and supplemental analyses panels are contained in this subfolder.
- All code to reproduce the analysis figure panels are contained in this subfolder.
- All code to reproduce the analysis figure panels are contained in this subfolder.
- All code to reproduce the analysis figure panels are contained in this subfolder.
For both ChIP-seq and RNA-seq followup analyses, we use the genome / transcriptome of HHV-6B available here
tree -L 2
.
├── README.md
├── hhv6-reference # folder relevant to HHV-6B annotations / references used in this manuscript
│ ├── AF157706_sequence.txt
│ ├── HHV6b_expression_annotations.tsv
│ ├── HHV6b_only.ec.txt
│ ├── HHV6b_only.index.txt
│ └── HHV6b_transcriptome.idx
├── public_bulk_data
│ ├── calderon-stim-immunecells-expression
│ ├── lamere-chipseq
│ ├── qu-atacseq
│ ├── richards-endothelial-CRS
│ ├── serratus-rnaseq-followup
│ ├── tcga # Preliminary analysis of OX40 expression in cancers
│ └── treg
└── single_cell_data # Data/analysis repositories for Fig. 2-4
├── broad-invivo # Folder for Fig 3 / cohort 2
├── cd7-cart # Folder for Fig 4
├── stanford-invitro # Folder for Fig 2
├── stjude-invitro # Folder for Fig 3 / in vitro reactivation
└── stjude-invivo # Folder for Fig 3 / cohort 3
Contact: Raise a GitHub issue or email Caleb or Ansu.