Transcriptomic Analysis of H. pylori

H. pylori NCTC 11637 strain grouping was the same as Genome DNA analysis and each group were run using three replicates. Total RNA was extracted with RNAprep Pure Cell/Bacteria kit (DP430, TIANGEN, China) and quality control was assessed using agar gel electrophoresis, NanoPhotometer spectrophotometer, and Agilent 2100 bioanalyzer for integrity and purity. Eligible RNA sample was treated with Ribo-Zero Magnetic kit (Bacteria) (Epicentre, USA) to remove rRNA. The cDNA library was constructed according to the Strand-specific approach (31 (link)). For the quality of the cDNA library, Qubit2.0 Fluorometer was used for preliminary quantification, and then qRT-PCR was used for accurate quantification to ensure its effective concentration was above 2 nM. Library construction and sequencing were conducted by Novogene Tech (Beijing) Co., Ltd. Raw reads were filtered and mapped to the H. pylori NCTC 11637 genome using Bowtie2. Gene expression counts were quantified using HTSeq. Differentially expressed genes (DEGs) were analyzed using DESeq2. Genes with absolute log₂-fold changes >0.5 and multiple P-value <0.05 were considered DEGs.