Computational protocol: High‐throughput identification of RNA nuclear enrichment sequences

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Protocol publication

[…] The phastCons and phyloP scores (Siepel et al, , ) for the whole genome were downloaded from UCSC genome browser. We extracted these scores for the DRs and shuffled control regions using a custom script. In order to account for natural conservation differences between lncRNAs and mRNAs as well as among different lncRNAs, the control regions were obtained by shuffling the DR sequences using shuffleBed but ensuring the new regions fell within exons of the lncRNAs the DRs were from. Finally, the scores were compared between DR and non‐DR regions using the Mann–Whitney test. [...] We downloaded the raw RNA‐Seq reads for the nucleus and cytosolic compartments from the ENCODE Project Consortium () website. These reads were quantified using salmon (Patro et al, ) to obtain TPMs, and then, the nuclear/cytosolic TPMs of transcripts with the motif [found using the FIMO (Grant et al, ) software] were compared to all the other transcripts for both lncRNAs and mRNAs. […]

Pipeline specifications

Software tools PHAST, MEME Suite
Applications RNA-seq analysis, Genome data visualization
Organisms Homo sapiens
Chemicals Cytosine