title: GSM2792947: HI broth + 25mM serine microaerophilic log; Campylobacter jejuni; RNA-Seq
library_construction_protocol: Total RNA was extracted from  cultures with the RNA-BeeTM kit (Tel-Test, Inc) according to the manufacturer’s specifications. . Subsequently, RNA was treated with RNAse-free DNaseI (Thermo) according to the instructions of the manufacturer. Ribozero Magnetic Kit for-gram negative bacteria (Illumina) following manufacturer’s instructions using following the 5ug RNA procedure and option 1 (Ethanol precipitation), except using 1/8th reaction volumes/amounts. Illumina libraries were prepared using the KAPA stranded RNA-seq kit (Kapa Biosystems, Wilmington, MA), following manufacturer’s instructions to produce ~300bp fragments. Standard desalting TruSeq LT primers were ordered from Integrated DNA Technologies (Coralville, IA) and used at 50-100nM final concentration based on starting RNA amount. The PCR step was reduced to 6 cycles. Libraries were quantified using the KAPA Library Quantification Kit (Kapa), except with 10 µl volume and 90 sec annealing/extension PCR. Libraries were pooled and normalized to 4 nM. Pooled libraries were re-quantified by ddPCR on a QX200 system (Bio-Rad), using the Illumina TruSeq ddPCR Library Quantification Kit and following manufacturer’s protocols. The libraries were sequenced in two 2x76bp paired end v3 runs on a MiSeq instrument (Illumina) at 13.5 pM, following manufacturer's protocols.