Bulk RNAseq raw count data of antibody-induced syncytia during SARS-CoV-2 infection

For cell type-specific RNA-seq analysis, Caco2-3a-E cells were first labeled with 5 µM of eFluor450 dye before seeding. Then Caco2-3a-E cells were infected with DORF3a-E mNG (MOI=1), incubated with GW01 (1 µg/mL, 30 min) and co-cultured with THP-1 cells for 24 h as described above. The cells were then harvested, stained with CD64-APC antibody, and sorted using a FACS Aria III into three populations: syncytia (eFluor450+ APC+), unfused Caco2-3a-E (eFluor450+ APC-) and unfused THP-1 cells (eFluor450- APC+). Total RNAs were extracted (Cat# 74134, Qiagen) and libraries were constructed (Cat# 20020189, Illumina) per manufacturer’s instructions. After quality and quantity assessment of the libraries, RNA-seq samples were sequenced with Illumina Novaseq X plus instrument (pair-end 150 cycle reactions). The reads with the adaptor or low-quality sequences were firstly removed from the raw fastq data using trimmomatic (version 0.36). Secondly, clean reads were aligned to Ensembl GRCh38 using STAR(version 2.7.0) with default parameters. Thirdly, we use featureCounts(version 2.0.1) to count the number of uniquely mapped read pairs for each gene.