Solexa gaiix genome analyzer

The study included 30 Korean Charcot-Marie-Tooth disease patients with whole exome data available from previous studies [14] (link), [15] (link). Written informed consent was obtained from all Korean participants according to the protocol approved by the Institutional Review Board of Ewha Woman’s University (Mokdong Hospital) and Korea National Institute of Health (KNIH).
The whole exome was captured from genomic DNA using the Human SeqCap EZ Human exome library v2.0 (Roche-NimbleGen, Madison, WI), and NGS was performed using the Solexa GAIIx Genome Analyzer (Illumina, San Diego, CA). Sequencing libraries were prepared following the standard Illumina library-preparation protocol for paired-end 76-bp reads. Raw ‘fastq’ files for both reads were generated and used for the alignment processes.

For the identification of strain SBV1, the 16S ribosomal RNA (rRNA) gene was amplified using primers 27F and 1492R (Table S1). The resulting product was subsequently purified using the PCR Purification Kit (Qiagen) and sequenced by GATC Biotech. The nucleotide sequence was deposited at GenBank (accession number KM657826). Subsequent identification was performed online, using the EzTaxon database (Chun et al. 2007 (link)).
In order to obtain a partial sequence of the SBV1 genome, total genomic DNA from SBV1 cells grown on MM containing 10 mM β-valine and 20 mM glucose was isolated according to a described procedure (Poelarends et al. 1998 (link)). The resulting genomic DNA was subjected to paired-end sequencing by Baseclear BV. The genome sequencing was done using an Illumina (Solexa) GAIIx Genome Analyzer. Sequencing yielded 7.2 million reads of ~50 bp. These were assembled using the CLC Genomics Workbench software, resulting in 996 contigs with a total length of 6,440,520 bp.
Sequencing of pLAFR3 inserts from specific P. fluorescens Pf0-1 transconjugants was done at GATC Biotech, using various primers. The complete insert sequence of p4-D1 was assembled by combining the contigs of the partial genome sequence and primer walking (GATC Biotech), resulting in a sequence of 25,618 bp (GenBank accession number KM595283).