AB 5500xl Genetic Analyzer sequencing; RNA-seq of Cellulophaga baltica phage 18:3 infection
RNA-seq of Cellulophaga baltica phage 18:3 infection
Bacterial isolates C. baltica strains #18 and NN016038 and phages phi38:1 and phi18:3 used in this study were previously isolated and characterized(Holmfeldt, Middelboe et al. 2007, Holmfeldt, Solonenko et al. 2013, Holmfeldt, Howard-Varona et al. 2014, Dang, & Howard-Varona et al. 2015), and the genomes are publicly available: C. baltica #18 (originally at GenBank # CP009976 and refined at https://de.cyverse.org/de/?type=data&folder=/iplant/home/shared/iVirus/ /Cellulophaga_Transcriptomics/Cellulophaga_baltica_strain#18), C. baltica NN016038 (GenBank # CP009887.1), phi18:3 (Genbank # NC_021794.1), phi38:1 (originally at GenBank # NC_021796.1 and refined at https://de.cyverse.org/de/?type=data&folder=/iplant/home/shared/iVirus/ /Cellulophaga_Transcriptomics/).  RNA extractions were performed with the RNeasy Mini Kit (Qiagen cat. no. 74104), DNase treated with TURBO DNA-free (Ambion AM1907) and concentrated to 20 μl with the RNA Clean and Concentrator -5 kit (Zymo Research R1015). The RNA integrity number (RIN) and concentration of the extracted RNA was determined via the Agilent Bioanalyzer 2100 (Agilent Technologies, USA).Libraries of complementary DNA were prepared for SOLiD 5500 XL (Applied Biosystems) sequencing according to the manufacturer’s protocol (Life Technologies, USA).