miRNA-Seq from plasma extracellular vesicles of rhesus macaques
Each library was indexed using a unique barcode for multiplexing and sequenced on the NextSeq2000 or Hiseq4000 platform (Illumina, San Diego, CA) to yield single-end 100 bp sequences. Quality reports for the raw miRNA reads were generated using FASTQC. The reads were trimmed 10-50 bp. Followed by alignment to the Macaca mulatta genome from Ensembl using splice aware short read aligner suite Bowtie 2 (45). The transcript counts per gene were then summarized using the summarizeOverlaps function. Samples were required to have a minimum of 1,500,000 reads post alignment and 400 detected miRNA to ensure good coverage of the genome.