Gs flx standard nebulizer kit

15.0 mL of sludge obtained from the bioreactor digesting freeze dried Spirulina were used for DNA extraction (sampling day 336, biogas production, 1676 mL biogas day⁻¹, methane content 60 %). DNA was extracted according to Zhou et al. [53 (link)] with minor modifications. 2.5 μg of extracted DNA were used to prepare a 200 bp insert size sequencing library for the Ion Torrent Personal Genome Machine (PGM) platform (Life Technologies, USA). The instructions according to the Ion Xpress™ - Plus gDNA Fragment Library Preparation manual were followed, except for the initial DNA fragmentation, which was done using a GS FLX Standard Nebulizer Kit (Roche Applied Science, Germany), nebulization for 3 min at 32 psi. Sequencing template preparation was performed using the OneTouch Instrument and the OneTouch ES module. Enriched ISP particles were sequenced with the Ion PGM™ 200 Sequencing Kit (Life Technologies, USA) on a 318™ Chip with 520 flows following the manufacturer’s instructions. Automated analysis was performed with the Torrent Suite™ Software v3.2 using default settings. Additional quality filtering was done using the Trimmomatic tool v3 (http://www.usadellab.org/cms/index.php?page=trimmomatic) [54 (link)], with settings for removal of trailing bases of a q-value lower than 20, and removal of reads shorter than 50 bases.

2.5 μg of purified extracted DNA were used to prepare a 400 bp insert size sequencing library for the Ion Torrent Personal Genome Machine (PGM) platform (Life Technologies, USA). The instructions according to the Ion Xpress™—Plus gDNA Fragment Library Preparation manual were followed, except for the initial DNA fragmentation, which was done using a GS FLX Standard Nebulizer Kit (Roche Applied Science, Germany), nebulization for 3 min at 32 psi.
For cDNA library preparation, the “Ion Total RNA-seq kit v2 for whole transcriptome libraries” was used. 20 ng mRNA of the sample were used to prepare the cDNA library. Sequencing template preparation was performed using the OneTouch Instrument. Enriched ISP particles were sequenced with the Ion PGM™ 400 Sequencing Kit (Life Technologies, USA) on a 318™ Chip with 1,000 flows for both the DNA and cDNA sequencing, following the manufacturer's instructions.
Automated quality control of the sequenced reads was performed with the Torrent Suite™ Software v3.2 using default settings. Additional quality filtering was done using the Trimmomatic tool v3 (http://www.usadellab.org/cms/index.php?page=trimmomatic) (Lohse et al., 2012 (link)) with settings for removal of trailing bases of a q-value lower than 20, and removal of remaining reads shorter than 100 bp and longer than 450 bp for DNA and shorter than 20 bp and longer than 350 bp for cDNA.