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Janjic, Aleksandar; Wange, Lucas E.; Bagnoli, Johannes W.; Geuder, Johanna; Nguyen, Phong; Richter, Daniel; Vieth, Beate; Vick, Binje; Jeremias, Irmela; Ziegenhain, Christoph; Hellmann, Ines and Enard, Wolfgang (31. March 2022): Prime-seq, efficient and powerful bulk RNA sequencing. In: Genome Biology, Vol. 23 [PDF, 2MB]


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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