FZ_VEEV_counts_and_cell_metadata.zip (28.82 MB)
The transcriptional landscape of Venezuelan equine encephalitis virus infection
datasetposted on 2020-02-19, 21:33 authored by Fabio ZaniniFabio Zanini, Zhiyuan Yao, Nuttada Panpradist, Sathish Kumar, Shirit Einav, Stephen QuakeStephen Quake
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