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1 1 1 This protocol described the procedures of analyzing RNA-Seq data for the expression of long non-coding RNAs (lncRNAs) as well as protein-coding genes (PCGs), as well as identifying the genomic location of lncRNAs and lncRNA-PCG pairs. As an example, we used an existing RNA-Seq dataset generated in our labotratory, which were deposited in Gene Expression Omnibus (GEO) database (accession number: GSE101650) and are available to the public. Li CY, Cui JY (2018) Regulation of protein-codingdoi:10.17504/protocols.io.n2tdgen fatcat:4bv2gmkgw5bibbcpnn3ph5leni