GSM9144450: SOL-SHFD-2; Gallus gallus; RNA-Seq
Total RNA was extracted from the PEM and SOL muscles using TRIzol reagent (Invitrogen, USA). RNA concentration and purity were assessed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA), and RNA integrity was confirmed via agarose gel electrophoresis (Biowest, France) and the Agilent 2100 Bioanalyzer (Agilent Technologies, USA). All samples met the quality requirements for RNA sequencing, with concentrations ≥300 ng/μL, RNA integrity number (RIN) >7.0, and OD260/280 ratios between 1.8 and 2.2. Each group included four biological replicates. Raw reads were filtered using fastp to remove adapters and low-quality sequences. Clean reads were mapped to the chicken reference genome (GRCg6a, Ensembl release April 2022) using HISAT2. Transcript assembly and quantification were performed with StringTie (v1.3.3b), and expression levels were calculated as fragments per kilobase of transcript per million mapped reads (FPKM).