Engineered probiotic restores glp-1 signaling to ameliorate fiber-deficiency-exacerbated colitis

Raw sequencing data were first processed through Novogene’s quality control (QC) pipeline, in which raw reads were filtered to remove adapter sequences, ambiguous bases (N > 10%), and low-quality reads (reads with >50% bases having a quality score ≤ 5). Clean reads obtained from this step were then aligned to the reference genome using HISAT2, allowing precise mapping of splice junction reads and comprehensive detection of differential gene expression, alternative splicing events, genetic variants, and gene fusions. Post-mapping analyses included quantification and annotation of gene expression levels, normalized as fragments per kilobase of transcript per million mapped reads (FPKM). Genes were annotated with detailed genomic attributes such as chromosome location, strand orientation, gene length, biotype, transcription factor families, and functional descriptions. All QC information, stats and analysis including reads count and FPKM used for further analysis are uploaded here.