R scripts for CSF scRNAseq and blood and CSF bulk RNAseq analysis associated with the publication "Contribution of cytotoxic CD8 T cells, neutrophils and type 1 interferon signaling to hyperinflammation in HIV-associated TB meningitis"
Authors list
James Barnacle Hubert Slawinski Christopher Barrington Katalin Wilkinson Rachel Lai Angharad Davis Anne O'Garra Robert WilkinsonAbstract
This software project contains the R scripts used to analyse CSF single cell RNA sequencing data, CSF bulk RNA sequencing data, and blood bulk RNA sequencing data presented in the manuscript "Contribution of cytotoxic CD8 T cells, neutrophils and type 1 interferon signaling to hyperinflammation in HIV-associated TB meningitis".The scRNAseq data in this manuscript come from day 7 CSF samples of HIV-TBM patients enrolled in the INTENSE-TBM trial from 2023-2024. Samples were fixed in Cape Town, stored up to 12 months, and processed at the Francis Crick Institute. Samples were sequenced in 3 batches; a pilot (n=4), batch 2 (n=10), and batch 3 (n=11). Two samples in batch 3 were double barcoded giving double the number of cells.The bulk RNA sequencing data is from blood and CSF samples taken from INTENSE-TBM and LASER-TBM participants and includes up to 6 timepoints. These samples were also collected in Cape Town and sequenced at the Francis Crick Institute. For further method details please see the manuscript.Raw fastq files and processed CSF scRNAseq data, CSF bulk RNAseq and blood bulk RNAseq are deposited in the GEO at accessions GSE321718, GSE324044 and GSE324265, respectively. For more details about the R scripts please see the README.txt file.
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Figshare
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