mNGS of human cerebrospinal fluid metagenome
The volume of CSF used for DNA extraction was 1.2 mL. An NGS Automatic Library Preparation System (Cat. MAR002, MatriDx Biotech Corp., Hangzhou, China) was used to automate DNA extraction and library preparation. The accompanied kits were a Nucleic Acid Extraction Kit (Cat. MD013, MatriDx Biotech Corp.) and a Total DNA Library Preparation Kit (Cat. MD001T, MatriDx Biotech Corp.). The Agilent 2100 Bioanalyzer System (Agilent Technologies, United States) was used to quality control the prepared libraries (PCR-free), and adapters-specific quantitative PCR was used to quantify them. The libraries were then adjusted (aiming for 20 million (M) reads) and pooled for NGS on an Illumina NextSeq550Dx system using the sequencing strategy of single-end (SE) 50 base pairs (bp). For contamination control, irrelevant cell line-based control samples were used throughout the process (in parallel with CSF samples).