Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2
Top Cited Papers
- 6 December 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Biotechnology
- Vol. 39 (3), 313-319
- https://doi.org/10.1038/s41587-020-0739-1
Abstract
Measurement of the location of molecules in tissues is essential for understanding tissue formation and function. Previously, we developed Slide-seq, a technology that enables transcriptome-wide detection of RNAs with a spatial resolution of 10 mu m. Here we report Slide-seqV2, which combines improvements in library generation, bead synthesis and array indexing to reach an RNA capture efficiency similar to 50% that of single-cell RNA-seq data (similar to 10-fold greater than Slide-seq), approaching the detection efficiency of droplet-based single-cell RNA-seq techniques. First, we leverage the detection efficiency of Slide-seqV2 to identify dendritically localized mRNAs in neurons of the mouse hippocampus. Second, we integrate the spatial information of Slide-seqV2 data with single-cell trajectory analysis tools to characterize the spatiotemporal development of the mouse neocortex, identifying underlying genetic programs that were poorly sampled with Slide-seq. The combination of near-cellular resolution and high transcript detection efficiency makes Slide-seqV2 useful across many experimental contexts.Funding Information
- U.S. Department of Health & Human Services | National Institutes of Health (DP2 AG058488-01, 1DP5OD024583)
- U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (R01HG010647, R01HG010647)
- Burroughs Wellcome Fund
This publication has 46 references indexed in Scilit:
- In situ sequencing for RNA analysis in preserved tissue and cellsNature Methods, 2013
- STAR: ultrafast universal RNA-seq alignerBioinformatics, 2012
- clusterProfiler: an R Package for Comparing Biological Themes Among Gene ClustersOMICS: A Journal of Integrative Biology, 2012
- Stickler syndrome, ocular-only variants and a key diagnostic role for the ophthalmologistEye, 2011
- The Dendritic Branch Is the Preferred Integrative Unit for Protein Synthesis-Dependent LTPNeuron, 2011
- Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA NanoarraysScience, 2010
- Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encodingGenome Research, 2009
- Making synaptic plasticity and memory last: mechanisms of translational regulationGenes & Development, 2009
- Imaging individual mRNA molecules using multiple singly labeled probesNature Methods, 2008
- A Direct Approach to False Discovery RatesJournal of the Royal Statistical Society Series B: Statistical Methodology, 2002