The Expression Ratio (HN-ratio) of Gene Expression Under Heat-stress and Non-stress Conditions in Human and Mouse.

After quantifying expression using the analysis pipeline ikra (https://github.com/yyoshiaki/ikra), expression ratios (HN-ratios) were calculated for data collected in pairs of HS and non-treatment conditions. The HN-ratios calculated for all genes were then classified as "upregulated," "downregulated," or "unchanged" if neither threshold was met, according to a defined threshold (5-fold or 1/5-fold in this study). This classification facilitates the interpretation of complicated gene expression data.<br>Gene expression data retrieval, processing, and quantification were performed using ikra (ver. 2.0.1), an automated human and mouse RNA-seq data analysis pipeline. Ikra is a tool that can automatically perform all the following processes: retrieval of FASTQ format files using the fasterq-dump program in the NCBI SRA tool kit (ver. 3.0.0), read quality control, and adapter trimming using Trim_galore (ver. 0.6.6) and transcript quantification using Salmon (ver. 1.9.0). The reference sequence sets of human GENCODE Release 37 (GRCh38.p13) and mouse GENCODE Release 26 (GRCm39) were used. HN-ratio was calculated using codes used in previous papers (https://github.com/no85j/hypoxia_code).<br>