Metagenomics data for IVCC samples from fermentor F7 with treatment 5NIT
The DNA was extracted using ZymoBIOMICS MagBead DNA/RNA kit with ZR BashingBead Lysis tubes following manufacturers instructions (Zymo Research, Irvine, CA, USA). Genomic DNA was quantified using the Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA). NEBNext Ultra II DNA Library Prep Kit for Illumina was used for library preparation, following the manufacturers recommendations. Briefly, the genomic DNA was fragmented by acoustic shearing with a Covaris S220 instrument. Fragmented DNA was cleaned and end-repaired. Adapters were ligated after adenylation of the 3ends, followed by enrichment by limited cycle PCR. DNA libraries were validated using a High Sensitivity D1000 ScreenTape on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA). The DNA libraries were also quantified by real-time PCR (Applied Biosystems, Carlsbad, CA, USA). The sequencing libraries were clustered onto a 25B flowcell on the Illumina NovaSeq X Plus instrument according to the manufacturers instructions. The samples were sequenced using a 2x150 paired-end configuration, targeting ~3 Gb/sample. The control software conducted image analysis and base calling. Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.