GSM5462566: MT_CK_1; Salmonella enterica subsp. enterica serovar Typhimurium; RNA-Seq
RNA was extracted using TRIzol Reagent (Invitrogen, CAS 15596026) according to the manual.RNA quality and integrity was verified by electrophoretic analysis and UV spectroscopy using NanoDrop and Agilent 2100 instruments. The RNA integrity number for all samples were between 8.2 and 9.7. The Strand-specific transcriptome library construction and RNA sequencing was done as follow. Briefly, 1 µg total RNA was digested with DNase I (Thermo Scientific) and treated with Ribo-Zero Magnetic Gold Kit (Epicenter) to deplete rRNA. The protocol of TruSeq RNA Sample Prep Kit v2 (Illumina) was used to construct the libraries. The RNA was fragmented into small pieces and first-strand cDNA was generated using Super Script II (Invitrogen). The products were purified and used in a Second Strand Master Mix containing dATP, dGTP, dCTP and dUTP. The purified fragmented cDNA was end-repaired and purified and A-tailed and adapters were attached. The purified product was digested with uracil-N-glycosylase to remove the dUTP containing second strand cDNA, followed by several rounds of PCR amplification to enrich the cDNA fragments. The PCR products were purified and the libraries were assessed using the Agilent 2100 Bioanalyzer and qPCR.