Syncytiotrophoblast Membrane Extracellular Vesicles (STB-EVs) Derived Transcriptomic Biomarkers of Preeclampsia-Supplemental Data
The folder includes the complete list of differentially expressed genes and functional enrichment analysis (Gene Ontology; Biological Processes (GO:BP), Molecular Functions (GO:MF), Cellular Components (GO:CC), SPIA, and KEGG Pathways) of placenta, medium/large syncytiotrophoblast membrane extracellular vesicles (m/lSTB-EVs), and small STB-EVs in preeclampsia.
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We performed bioinformatics analysis on Galaxy (https://usegalaxy.org/). We used FastQC (Galaxy Version 0.72+galaxy1) to obtain overall QC metrics and MultiQC (Galaxy Version 1.9+galaxy1) to amalgamate the QC metrics before and after trimming of adapters [trimmomatic (Galaxy Version 0.38.0)]. Alignment was referenced to reference Homo Sapiens build 38 (hg38) genomes obtained from Ensembl with HISAT 2 (Galaxy Version 2.2.1+galaxy0). For each sample, featureCounts (Galaxy Version 2.0.1+galaxy1) was used to quantify genes based on reads that mapped to the provided hg38 genome. A count matrix was generated with the Column Join on Collection (Galaxy Version 0.0.3) tool. Differential expression analysis was done with the DESeq2 package (v.1.32.0 in R v.4.0.5). The reported p-values were adjusted for multiple testing using Benjamin Hochberg correction reported as false-discovery rate. An adjusted p-value less than 0.05 was taken as significant. Functional annotation was performed with ClusterProfiler (for Gene Ontology [GO] and KEGG) and Signalling pathway impact analysis (SPIA) with our transcriptome set as the background. The raw fastQ files and processed file have been deposited in NCBI and can be accessed with the following ID: GSE190973.