RNA-Sequencing of whole blood from non-human primate-neonate exposed to SARS-CoV-2.

Frozen whole blood Tempus samples from a non-human primate neonate exposed to SARS-CoV-2 (different time-points available), were processed for RNA extraction, processing and sequencing (Oxford Nanopore Technologies, Oxford, UK). Samples were quantified then loaded on R9.4.1 Flow cells using GridION instrument. Sequence reads were converted into FASTQ files. Reads under 100bp or with a quality score under seven were discarded. Remaining reads were aligned on Macaca mulatta transcriptome of reference (GeneBank assembly accession number GCA_003339765.3) using minimap2 version 2.17. To quantify transcripts, the resulting alignments were given to Salmon version 1.4.0. To explore single replicates, samples were duplicated to use DESeq2 version 1.32.0.