cucumber rhizosophere illumina paired end whole genome shotgun metagenome samples
Genomic DNA extracted from soils and rhizosphere were processed for metagenomic sequencing using a Nextera dual-indexed DNA sample preparation kit, according to the manufacturer’s instructions (Illumina Inc, San Diego, CA). 50 ng of genomic DNA were used as input, and after processing and purification, library fragments of 400-800 bp in size were selected using a PippinPrep automated electrophoresis device (Sage Science, Beverly, MA). Individual libraries were quantified using the KAPA library qPCR quantification kit for Illumina (KAPA Biosystems, Woburn, MA), pooled in equimolar ratio, and purified again. The final library concentration was adjusted to 10 nM after a subsequent quantification reaction. Libraries were sequenced on an Illumina HiSeq2000 instrument, with paired-end 100 base reads. In total, 410-527 M reads (combined forward and reverse reads) were recovered from each lane.