si_NC_2 rep1
The RNA sequencing data underwent basecalling with Illumina Casava 1.7 software. Trimmomatic (Version 0.36) was employed to remove adapter sequences, followed by alignment using the Hisat2 aligner. Post-alignment, duplicates were marked, and the data was sorted and indexed with Samtools. Differential expression analysis was conducted using Partek Genomic Suite (PGS, MO, USA), and transcripts per million (TPM) normalization was performed for each sample. Statistical analysis included group-wise comparison and FDR p value correction using the Benjamini Hochberg method. Functional analysis was carried out with Ingenuity Pathway Analysis (IPA, Qiagen, USA), and the genome reference used was hg19. Supplementary files in tab-delimited text format included TPM values for each sample. The reads were normalized in secondary analysis conducted in the R software environment.