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.