title: 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.
authors.affiliation: Science for Life Laboratory, Department of Gene Technology, Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
authors.forename: Anders
authors.initials: A
authors.lastname: Jemt
authors.affiliation: Science for Life Laboratory, Department of Gene Technology, Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Salmén
authors.affiliation: Department of Dental Medicine, Division of Periodontology, Karolinska Institutet, SE-141 04, Huddinge, Sweden.
authors.forename: Anna
authors.initials: A
authors.lastname: Lundmark
authors.affiliation: Science for Life Laboratory, Department of Gene Technology, Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
authors.forename: Annelie
authors.initials: A
authors.lastname: Mollbrink
authors.affiliation: Science for Life Laboratory, Department of Gene Technology, Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
authors.forename: José
authors.initials: J
authors.lastname: Fernández Navarro
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
authors.forename: Patrik L
authors.initials: PL
authors.lastname: Ståhl
authors.affiliation: Department of Dental Medicine, Division of Periodontology, Karolinska Institutet, SE-141 04, Huddinge, Sweden.
authors.forename: Tülay
authors.initials: T
authors.lastname: Yucel-Lindberg
authors.affiliation: Science for Life Laboratory, Department of Gene Technology, Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
authors.forename: Joakim
authors.initials: J
authors.lastname: Lundeberg
mesh_terms: D057205:Automation, Laboratory; D058893:DNA Barcoding, Taxonomic; D015723:Gene Library; D005881:Gingiva; D006801:Humans; D010518:Periodontitis / Q000235:genetics* / Q000378:metabolism; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism
chemical_list: D012313:RNA