Illumina shotgun metagenomic sequencing ulcerative colitis microbiome study: Sample UC20021307M
"Metagenomic shotgun sequencing (Hiseq): We use Picogreen (Invitrogen) to quantitate genomic DNA samples. DNA is sheared using a Covaris and libraries were constructed with the Nugen Ovation Ultralow Library protocol. We aim for an insert size of 175bp to enable read merging. Amplified libraries are visualized on an Agilent DNA1000 chip or Caliper HiSens Bioanalyzer assay, pooled at equimolar concentrations based on these results, and size selected using a Sage PippinPrep 2% cassette. The library pool is quantified using a Kapa Biosystems qPCR library quantification kit, then sequenced on the Illumina HiSeq1000 in a 2x100 paired-end sequencing run using dedicated read indexing. The samples are demultiplexed with CASAVA 1.8.2.  Paired fastq files are raw data. Human_filtered.fastq.gz files have been quality filtered, merged (with a maximum of 3 mismatches in the region of overlap allowed), and screened for human genomic sequence. "