Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues.
Emelie Berglund,Sami Saarenpää,Anders Jemt,Joel Gruselius,Ludvig Larsson,Ludvig Bergenstråhle,Joakim Lundeberg,Stefania Giacomello +7 more
TLDR
This approach increases the number of samples processed per run, reduces sample preparation time by 35%, and minimizes batch effects between samples, and is also shown to be highly accurate and almost completely free from technical variability between prepared samples.Abstract:
Interest in studying the spatial distribution of gene expression in tissues is rapidly increasing. Spatial Transcriptomics is a novel sequencing-based technology that generates high-throughput information on the distribution, heterogeneity and co-expression of cells in tissues. Unfortunately, manual preparation of high-quality sequencing libraries is time-consuming and subject to technical variability due to human error during manual pipetting, which results in sample swapping and the accidental introduction of batch effects. All these factors complicate the production and interpretation of biological datasets. We have integrated an Agilent Bravo Automated Liquid Handling Platform into the Spatial Transcriptomics workflow. Compared to the previously reported Magnatrix 8000+ automated protocol, this approach increases the number of samples processed per run, reduces sample preparation time by 35%, and minimizes batch effects between samples. The new approach is also shown to be highly accurate and almost completely free from technical variability between prepared samples. The new automated Spatial Transcriptomics protocol using the Agilent Bravo Automated Liquid Handling Platform rapidly generates high-quality Spatial Transcriptomics libraries. Given the wide use of the Agilent Bravo Automated Liquid Handling Platform in research laboratories and facilities, this will allow many researchers to quickly create robust Spatial Transcriptomics libraries.read more
Citations
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Journal ArticleDOI
SM-Omics is an automated platform for high-throughput spatial multi-omics
Sanja Vickovic,Britta Lötstedt,Johanna Klughammer,Séverine Mages,Åsa Segerstolpe,Orit Rozenblatt-Rosen,Aviv Regev +6 more
TL;DR: SM-Omics as mentioned in this paper uses DNA-barcoded antibodies, immunofluorescence or a combination thereof, to scale and combine spatial transcriptomics and spatial antibody-based multiplex protein detection.
Posted ContentDOI
SM-Omics: An automated platform for high-throughput spatial multi-omics
Sanja Vickovic,Britta Lötstedt,Britta Lötstedt,Johanna Klughammer,Asa Segerstolpe,Orit Rozenblatt-Rosen,Aviv Regev,Aviv Regev,Aviv Regev +8 more
TL;DR: Spatial Multiomics (SM-Omics) is presented as a fully automated high-throughput platform for combined and spatially resolved transcriptomics and antibody-based proteomics.
Journal ArticleDOI
Unlocking the efficiency of genomics laboratories with robotic liquid-handling
TL;DR: The state-of-the-art technology of both sophisticated and do-it-yourself (DIY) robotic liquid-handlers are described and a practical review of the motivation, implications and requirements of laboratory automation for genome sequencing experiments is provided.
Journal ArticleDOI
Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium
Sanja Vickovic,Denis Schapiro,Konstantin Carlberg,Britta Lötstedt,Ludvig Larsson,Franziska Hildebrandt,Marina Korotkova,Aase Haj Hensvold,Anca I. Catrina,Peter K. Sorger,Vivianne Malmström,Aviv Regev,Patrik L. Ståhl +12 more
TL;DR: In this paper , spatial RNA-Seq data coupled with cell type-specific localization patterns at and around organized structures of infiltrating leukocyte cells in the synovium were used to study local tissue interactions at the site of chronic synovial inflammation.
Journal ArticleDOI
A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples.
Michal Kucharski,Jaishree Tripathi,Sourav Nayak,Lei Zhu,Grennady Wirjanata,Rob W. van der Pluijm,Rob W. van der Pluijm,Mehul Dhorda,Mehul Dhorda,Arjen M. Dondorp,Arjen M. Dondorp,Zbynek Bozdech +11 more
TL;DR: A comprehensive methodology on how to preserve, extract, amplify, and sequence full-length mRNA transcripts from Plasmodium -infected blood samples is presented that can be fully streamlined for high-throughput studies and will facilitate both small and large-scale future transcriptomic studies in the field of malaria.
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TL;DR: An anatomically comprehensive digital atlas containing the expression patterns of ∼20,000 genes in the adult mouse brain is described, providing an open, primary data resource for a wide variety of further studies concerning brain organization and function.