Tn5Prime, a Tn5 based 5′ Capture Method for Single Cell RNA-seq

Abstract

RNA-seq is a powerful technique to investigate and quantify entire transcriptomes. Recent advances in the field have made it possible to explore the transcriptomes of single cells. However, most widely used RNA-seq protocols fail to provide crucial information regarding transcription start sites. Here we present a protocol, Tn5Prime, that takes advantage of the Tn5 transposase based Smartseq2 protocol to create RNA-seq libraries that capture the 5′ end of transcripts. The Tn5Prime method dramatically streamlines the 5′ capture process and is both cost effective and reliable. By applying Tn5Prime to bulk RNA and single cell samples we were able to define transcription start sites as well as quantify transcriptomes at high accuracy and reproducibility. Additionally, similar to 3′ end based high-throughput methods like Drop-Seq and 10X Genomics Chromium, the 5′ capture Tn5Prime method allows the introduction of cellular identifiers during reverse transcription, simplifying the analysis of large numbers of single cells. In contrast to 3′ end based methods, Tn5Prime also enables the assembly of the variable 5′ ends of antibody sequences present in single B-cell data. Therefore, Tn5Prime presents a robust tool for both basic and applied research into the adaptive immune system and beyond.