Code associated with the analysis in the article: Microcephaly-like phenotype triggered by novel reassortant and prototypic Oropouche Virus strains in brain organoids
RNA-seq data analysis.
Raw FASTQ files quality were checked with FastQC and aligned against the human transcriptome (GENCODE v48)1 using Salmon2 with default parameters and Gibbs sampling bootstrap method. Transcript level quant files were imported into R and summarized to gene. Differential expression was performed with DeSeq23 and functional enrichment using R package fgsea4 against the Gene Ontology Biological process database (GOBP). Data wrangling and plotting was performed with Tidyomics5.
1 Mudge JM, Carbonell-Sala S, Diekhans M, et al. GENCODE 2025: reference gene annotation for human and mouse. Nucleic Acids Res 2025; 53(D1): D966–D975.
2 Patro R, Duggal G, Love MI, et al. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 2017; 14(4): 417–9.
3 Love MI, Huber W, Anders S, et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014; 15: 550.
4 Korotkevich G, Sukhov V, Budin N, et al. Fast gene set enrichment analysis. bioRxiv 2021; doi: 10.1101/060012.
5 Hutchison WJ, Keyes TJ, The tidyomics Consortium, et al. The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 2024; 21: 1166–70.