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An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.


ABSTRACT: Sequencing the nucleic acid content of individual cells or specific biological samples is becoming increasingly common. This drives the need for robust, scalable and automated library preparation protocols. Furthermore, an increased understanding of tissue heterogeneity has lead to the development of several unique sequencing protocols that aim to retain or infer spatial context. In this study, a protocol for retaining spatial information of transcripts has been adapted to run on a robotic workstation. The method spatial transcriptomics is evaluated in terms of robustness and variability through the preparation of reference RNA, as well as through preparation and sequencing of six replicate sections of a gingival tissue biopsy from a patient with periodontitis. The results are reduced technical variability between replicates and a higher throughput, processing four times more samples with less than a third of the hands on time, compared to the standard protocol.

SUBMITTER: Jemt A 

PROVIDER: S-EPMC5111054 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.

Jemt Anders A   Salmén Fredrik F   Lundmark Anna A   Mollbrink Annelie A   Fernández Navarro José J   Ståhl Patrik L PL   Yucel-Lindberg Tülay T   Lundeberg Joakim J  

Scientific reports 20161116


Sequencing the nucleic acid content of individual cells or specific biological samples is becoming increasingly common. This drives the need for robust, scalable and automated library preparation protocols. Furthermore, an increased understanding of tissue heterogeneity has lead to the development of several unique sequencing protocols that aim to retain or infer spatial context. In this study, a protocol for retaining spatial information of transcripts has been adapted to run on a robotic works  ...[more]

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