Characterizing the RNAs packaged by HIV-1. (A) After harvesting and concentrating by sedimentation, virions from HIV-infected (left panel) and control uninfected (right) CEM-SS cells were fractionated in iodixanol gradients. HIV-1-containing fractions were identified using RNase protection to detect HIV gRNA and 7SL RNA. Asterisks represent fractions used to prepare cDNA for RNA-seq. (B) Sequencing reads in the HIV-1 data set were aligned sequentially to the HIV-1 and human (hg19) genomes. The fraction of reads in each category is shown. (C) Overview of the alignment of reads from the HIV-1 data set to the human genome. RNAs in the “others” category include pseudogene transcripts and mitochondrial rRNA. (D) Alignment of reads from the uninfected control data set to the HIV and human genomes. (E) Overview of the alignment of reads from the control data set to the human genome.
