المؤلفون: Aleksandar Janjic, Lucas E. Wange, Johannes W. Bagnoli, Johanna Geuder, Phong Nguyen, Daniel Richter, Beate Vieth, Binje Vick, Irmela Jeremias, Christoph Ziegenhain, Ines Hellmann, Wolfgang Enard

المصدر: Genome Biology, Vol 23, Iss 1, Pp 1-27 (2022)

مصطلحات موضوعية: RNA-seq, Transcriptomics, Genomics, Power analysis, Biology (General), QH301-705.5, Genetics, QH426-470

الوصف: 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.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1474-760XTest

الوصول الحر: https://doaj.org/article/68399bd59d28488cb10eea8edd8b0b09Test

المؤلفون: Phong Nguyen, Ines Hellmann, Lucas E. Wange, Johannes W. Bagnoli, Daniel Richter, Irmela Jeremias, Christoph Ziegenhain, Wolfgang Enard, Johanna Geuder, Beate Vieth, Binje Vick, Aleksandar Janjic

المصدر: Genome Biol. 23:88 (2022)

مصطلحات موضوعية: Protocol (science), Profit (accounting), Base Sequence, Sequence Analysis, RNA, Computer science, genetic processes, RNA, computer.software_genre, Genomics, Power Analysis, Rna-seq, Transcriptomics, DNA sequencing, Prime (order theory), Statistical power, Exome Sequencing, natural sciences, RNA extraction, Data mining, computer, health care economics and organizations, Gene Library

الوصف: With the advent of Next Generation Sequencing, RNA-sequencing (RNA-seq) has become the major method for quantitative gene expression analysis. Reducing library costs by early barcoding has propelled single-cell RNA-seq, but has not yet caught on for bulk RNA-seq. Here, we optimized and validated a bulk RNA-seq method we call prime-seq. We show that with respect to library complexity, measurement accuracy, and statistical power it performs equivalent to TruSeq, a standard bulk RNA-seq method, but is four-fold more cost-efficient due to almost 50-fold cheaper library costs. We also validate a direct RNA isolation step that further improves cost and time-efficiency, show that intronic reads are derived from RNA, validate that prime-seq performs optimal with only 1,000 cells as input, and calculate that prime-seq is the most cost-efficient bulk RNA-seq method currently available. We discuss why many labs would profit from a cost-efficient early barcoding RNA-seq protocol and argue that prime-seq is well suited for setting up such a protocol as it is well validated, well documented, and requires no specialized equipment.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8fb9e8929a33ba0ce58e8fb3d5aaed50Test
https://doi.org/10.1186/s13059-022-02660-8Test