# Prime-seq, efficient and powerful bulk RNA sequencing

## TL;DR

Prime-seq is a cost-effective bulk RNA sequencing method that performs as well as standard methods but at a fraction of the cost.

## Contribution

Prime-seq is introduced as a fourfold more cost-efficient bulk RNA-seq method compared to TruSeq.

## Key findings

- Prime-seq performs equivalently to TruSeq but with significantly lower library costs.
- Intronic reads are confirmed to originate from RNA using the Prime-seq method.
- A direct RNA isolation step is validated for use with Prime-seq.

## Abstract

Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. Here, we optimize and validate prime-seq, an early barcoding bulk RNA-seq method. We show that it performs equivalently to TruSeq, a standard bulk RNA-seq method, but is fourfold more cost-efficient due to almost 50-fold cheaper library costs. We also validate a direct RNA isolation step, show that intronic reads are derived from RNA, and compare cost-efficiencies of available protocols. We conclude that prime-seq is currently one of the best options to set up an early barcoding bulk RNA-seq protocol from which many labs would profit.

The online version contains supplementary material available at 10.1186/s13059-022-02660-8.