1022 (CRX2037579; CRA030759)
the microbial DNA was extracted from 600 microL of CSF using a QIAamp UCP Pathogen DNA Kit (Qiagen, Valencia, CA, USA) following the manufacturer's instructions. After nucleic acid extraction, the isolated DNA was quantified using a Qubit dsDNA HS Assay Kit (Invitrogen, USA), and then libraries were constructed using a Nextera XT DNA Library Prep Kit (Illumina, San Diego, CA). Total RNA from CSF samples was extracted using the QIAamp Viral RNA Kit (Qiagen, Valencia, CA, USA), followed by human rRNA depletion using the Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions. After removing contaminating DNA with DNase I, cDNA was synthesized using reverse transcriptase and dNTPs. The Nextera XT DNA Library Prep Kit (Illumina) was then used to construct the cDNA library. Library concentration was measured using the Qubit dsDNA HS Assay Kit, and library quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using a High Sensitivity DNA kit. The libraries were sequenced on an Illumina NextSeq 550 sequencer for 75 cycles of single-end sequencing (Miller et al., 2019). submitted_instrument_model: Illumina Nextseq 550