Tracking adaptation at ultra-high resolution. Escherichia coli strain:DH5-alpha

E. coli DH5-alpha was transformed with the plasmid pBR322. One transformant was used as the founder strain throughout this project. This founder strain was expanded and seeded into turbidostat—a continuous culturing device which maintains constant cell density. Turbidostat contained LB medium supplemented with 30 µg/mL tetracycline and 0.05% antifoam B. Remaining culture of the seed was collected as the sample at time point 0. To establish time course of the adaptation approximately ⅔ of the volume (~8 ml) was sampled every 12 hours constituting time point 1, 2, 3, and so on. A total of four turbidostat replicates were conducted: two short-term (60 hours each with six collection points; replicates R1 and R2) and two long-term (318 hours each with 28 collection points; replicates R6 and R7).In R1 and R2, pBR322 was extracted from samples at time points 0, 1, 2, 3, 4, 5 and subjected to duplex sequencing. In R6 and R7, pBR322 was extracted from samples at time points 6, 7, 9, 13, 20, 27 and subjected to duplex sequencing. This generates 24 BioSamples, each linked to one duplex sequencing dataset in the SRA database. In addition, whole genomic DNA was extracted from samples of R6 and R7 at time points 0 and 27 and subjected to conventional high depth sequencing. This gives rise to 4 BioSamples, each linked to one regular sequencing dataset in SRA. All sequencing experiments were performed on an Illumina MiSeq platform using 301-bp paired-end reads. In total, 28 BioSamples are included in this BioProject. In term of BioSample and SRA dataset naming, for instance, R6-S0-duplex stands for duplex sequencing pBR322 from the sample in turbidostat replicate 6 at time point 0; R6-S0-WGS stands for whole genome sequencing the same sample.