RNA-seq Analysis of Knockdown Transcriptomes

RNA-sequencing was performed on 3 biological replicates of KD, DBD and DBD+. Total RNA were extracted using RNeasy Extraction Kit and submitted to the Nationwide Children’s Hospital Institute for Genomic Medicine for RNA quality measurement, library preparation, and sequencing. Briefly, cDNA libraries were prepared from total RNA with TruSeq Stranded mRNA Kit (Illumina 20020594) and sequenced on Illumina NovaSeq SP to generate 150-bp paired-end reads. We used in-house RNA-sequencing pipeline to process and analyze the data. Low-quality reads (q < 10) and adapter sequences were trimmed to align to hg19 genome using STAR (Dobin et al., 2013 (link)). After alignment, the reads were counted and differential analysis performed using DESeq2 (Love et al., 2014 (link)).