Abstract
BackgroundInterest 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.ResultsWe 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.ConclusionsThe 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.
Highlights
Interest in studying the spatial distribution of gene expression in tissues is rapidly increasing
Protocol description The ST library preparation protocol using the Bravo platform is a modification of the Spatial Transcriptomics method introduced by Ståhl et al in 2016 [38]
Tissue sections attached to the subarrays undergo fixation, histological staining, and tissue permeabilization, after which transcripts are captured by the surface probes and reverse transcribed overnight
Summary
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. Neither RNAseq nor scRNA-seq preserve the spatial information contained in the samples being studied, which is essential for understanding cell-cell interactions [16] To solve this problem, several spatially resolved transcriptomics approaches have been developed. Untargeted methods do not require to use gene-specific probes as they capture the whole spatial transcriptome information [22,23,24,25] They enable high-throughput studies, and can be used to study less well-characterized organisms [26]. After cDNA synthesis on the surface, the tissue is removed and the mRNA-cDNA hybrids are released from the array to be prepared for sequencing
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
