Construction of transcriptional regulatory networks using total RNA-seq data

Total RNA sequencing allows capturing of long non-coding and circular RNA along with mRNA. Additional sequencing of micro RNA (miRNA), using libraries with shorter fragments, provides the means to characterize miRNA-driven transcriptional regulation. Here, we present a protocol for processing total RNA and miRNA sequencing data to quantify circular RNA, long non-coding RNA, mRNA, and miRNA. Further, the protocol combines the quantification data with miRNA target annotation to construct likely transcriptional regulatory networks, which can be validated in the subsequent studies. For complete details on the use and execution of this protocol, please refer to Chouvarine et al. (2021).