title: G4000 E. coli
design: Total genomic DNA for each sample was isolated using the GenEluteTM Bacterial Genomic DNA kit (Sigma Aldrich). Next-generation sequencing library preparations were carried out following the manufacturers protocol (NEBNext UltraTM DNA Library Prep Kit for Illumina). For each sample, 1 g genomic DNA was randomly fragmented to <500 bp by sonication (Covaris S220). The resulting fragments underwent treatment with End Prep Enzyme Mix for end repairing, 5 Phosphorylation, and dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~410 bp (with an approximate insert size of 350 bp) were recovered. Each sample was then amplified by PCR for 8 cycles using P5 and P7 primers, with both primers carrying sequences that can anneal with the flowcell to perform bridge PCR, and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA). Subsequently, libraries with different indexes were multiplexed and loaded on an Illumina HiSeq instrument according to the manufacturers instructions (Illumina, San Diego, CA, USA).