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

Prime-seq, efficient and powerful bulk RNA sequencing.

Genome Biol. 23:88 (2022)

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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.

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