Cited by 1,295Single-cell and spatial transcriptomicsRNA Research and SplicingMolecular Biology Techniques and Applications

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

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Stickels, Robert R., Murray, Evan, Kumar, Pawan, Li, Jilong, Marshall, Jamie L., Di Bella, Daniela J., Arlotta, Paola, Macosko, Evan Z. +1 more·2021·Nature Biotechnology

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 μm. Here we report Slide-seqV2, which combines improvements in library generation, bead synthesis and array indexing to reach an RNA capture efficiency ~50% that of single-cell RNA-seq data (~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.

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  • Slide-seq and Slide-seqV2 barcode mRNA using barcoded reagents placed directly on glass slide in solution, creating a monolayer-packed array.

    “Slide-seq, and later Slide-seqV2, barcode mRNA in tissues using a method conceptually similar to spatial transcriptomics, but a different strategy: instead of using arrayed barcoded reagents printed on slides, the barcoded reagents are placed directly onto the glass slide in solution, thereby creating a monolayer-packed array on a glass coverslip118,119 (Fig. 4a).”

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  1. [10]Hughes TK, Wadsworth MH, Gierahn TM & Do T Highly efficient, massively-parallel single-cell RNA-seq reveals cellular states and molecular features of human skin pathology. bioRxiv (2019).

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Authors
Stickels, R. R., Murray, E., Kumar, P., Li, J., Marshall, J. L., Di Bella, D. J., Arlotta, P., Macosko, E. Z., & Chen, F.
Affiliations
  • Broad Institute (US)
  • Massachusetts General Hospital (US)
Corresponding author
  • Macosko, Evan Z.
  • Chen, Fei
Venue
Nature Biotechnology
Published
2020-12-07
Volume
39
Issue
3
Pages
313-319
ISSN
  • 0733-222X (ISSN-L)
  • 1087-0156
  • 1546-1696
OpenAlex
W3112563877
Cited by
1,295
References
47
Citations by year
2026: 247 · 2025: 277 · 2024: 304 · 2023: 192 · 2022: 186 · 2021: 88
FWCI
38.93
Type
journal article
Language
en
Open access
Locations
  • Nature Biotechnology (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion)
Funders
  • 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)
  • Burroughs Wellcome Fund
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
Keywords
spatial transcriptomics, dendritic mRNA localization, hippocampal neurons, neocortex development, spatiotemporal gene expression, single-cell trajectory analysis, array indexing, library construction
MeSH terms
Animals, Humans, RNA, Messenger, Sequence Analysis, RNA, Mice, Single-Cell Analysis, Transcriptome

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