| We transiently transfected uninfected iSLK cells, a renal carcinoma-derived cell line that carries no KSHV, with a plasmid expressing the KSHV long noncoding RNA ALT (pcDNA-ALT) or with the empty pcDNA vector, and harvested the cells 72 hours after transfection. All samples come from this single time point, so there is no time variable. | |
| The plasmid is in the `group` column: ALT_plasmid means transfected with pcDNA-ALT, and control_plasmid means transfected with the empty vector. There are three samples per plasmid, and each sample is one independently transfected iSLK culture; all six come from the same cell line, but no two come from the same culture. The letters A, B and C and the numbers in `sample_id` only count the transfections within each plasmid; there is no record that an ALT and a control transfection with the same letter were done together or are related in any other way. Each library was sequenced once; there are no technical replicates. | |
| We have no record of processing or sequencing batches and no other variable we consider relevant; the remaining columns are the same for all samples. The data are bulk total RNA-seq after rRNA depletion, given as gene-level integer counts of human genes. The 96 KSHV gene features and the ALT feature were removed from the matrix, because our interest is in the host genes. | |
| Our question is which human genes are differentially expressed in ALT-transfected cells (ALT_plasmid) compared with empty-vector-transfected cells (control_plasmid). | |