Long-read RNA sequencing of transposable elements from single cells using CELLO-seq

Transposable elements (TEs) form 50% of the mammalian genome sequence, and their expression contributes to processes from development to disease. Owing to the abundance and high sequence similarity of TEs, short-read single-cell sequencing methods promote ambiguous mapping to many almost-identical TE loci across the genome. Here we present a protocol for single-cell long-read RNA sequencing (CELLO-seq) to enable the mapping of TE-derived reads to unique genomic loci. CELLO-seq enables the error correction of long reads through the incorporation of long 50-nucleotide unique molecular identifiers and high polymerase chain reaction duplicate numbers. Taken together, these features of CELLO-seq enable the high-fidelity mapping of expression data to highly sequence-similar young TEs, as well as to gene and TE isoforms. This will enable in-depth exploration into the interaction of individual TEs and genes within single cells. This Protocol is designed to be accessible for users with experience in molecular biology and transcriptomic analysis and can be completed within a week from cell isolation through to quantification.