Anthropology and Human Genetics

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Prime-seq, efficient and powerful bulk RNA-sequencing

by A. Janjic, L. E. Wange, J.W. Bagnoli, J. Geuder, P. Nguyen, D. Richter, B. Vieth, B. Vick, I. Jeremias, C. Ziegenhain, I. Hellmann & W. Enard



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.

Publication in Genome Biology.

Protocol freely available on