S4 100pe flowcell

The details of RNA extraction, RNA-sequencing, quality control, and transcriptome profiling are described in the Supplemental Methods. Briefly, after total RNA extraction, DNase treatment, and ribosomal RNA reduction, we performed RNA-sequencing with NovaSeq6000 (Illumina, San Diego, CA, USA) using an S4 100PE Flowcell (Illumina, San Diego, CA, USA). All RNA-sequencing samples had high sequence coverage after quality control. The transcript abundances were estimated with Salmon using the human genome hg38 and the mapping-based mode [28 (link)].

The details of RNA extraction, RNAseq, and quality control are described in the Supplementary Methods. Briefly, after total RNA extraction, DNase treatment, and rRNA reduction, we performed RNAseq with Illumina NovaSeq6000 using an S4 100PE Flowcell (Illumina, San Diego, CA). All RNAseq samples had high sequence coverage (a mean of 8,067,019 pair-end reads/sample) after quality control. We filtered and trimmed raw reads for adapters and contaminants using the k-mers strategy in bbduck. We characterized the active (via RNA transcripts) bacterial component of the microbiome (species-level) coupling PathoScope 2.0 with the expanded Human Oral Microbiome Database. To characterize the microbiome function, we used SUPER-FOCUS and Diamond. To annotate proteins that implement a specific biological process or structural complex into subsystems, we used the SEED database. This database comprises three-level hierarchical microbiome functions: the level 1 subsystem with 35 functions, followed by the level 2 subsystem with 194 functions and the level 3 subsystem with 1,290 functions. Lastly, we estimated host transcript abundances in Salmon using the human genome (hg38) and the mapping-based mode.