The transcriptional landscape of Venezuelan equine encephalitis virus infection

U87 human cells were infected with GFP+ Venezuelan Equine Encephalitis Virus (VEEV) strain TC-83 with 3 MOIs (0.1, 1, 3) and harvested at 6 time points (0.5 - 24 hours post infection). viscRNA-Seq was performed as in Zanini F, Pu SY, et al. eLife (2018).

The file is a zip archive containing two files:

- counts table with the gene expression of human genes, VEEVGFP, ERCC spike-in RNA controls, and other features from the aligner (e.g. unmapped reads). The counts are unnormalized, raw read pair numbers.

- cell_metadata table with the following columns:

- coverage: total number of uniquely mapped human reads

- VEEV_counts: total number of viral reads

- plate: microtiter plate each cell was sorted into (to spot batch effects)

- well: the well within each plate each cell was sorted into

- time [h]: time post infection

- vRNA_5' [cpm]: viral reads in bases 1-1700 of the viral genome, normalized by human coverage per million reads

- vRNA_3' [cpm]: viral reads in bases 7501+ of the viral genome, normalized by human coverage per million reads