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Spatially mapped single-cell chromatin accessibility

Author

Listed:
  • Casey A. Thornton

    (Oregon Health & Science University)

  • Ryan M. Mulqueen

    (Oregon Health & Science University)

  • Kristof A. Torkenczy

    (Oregon Health & Science University)

  • Andrew Nishida

    (Oregon Health & Science University)

  • Eve G. Lowenstein

    (Oregon Health & Science University)

  • Andrew J. Fields

    (Oregon Health & Science University)

  • Frank J. Steemers

    (Illumina Inc.)

  • Wenri Zhang

    (Oregon Health & Science University)

  • Heather L. McConnell

    (Oregon Health & Science University)

  • Randy L. Woltjer

    (Oregon Health & Science University)

  • Anusha Mishra

    (Oregon Health & Science University
    Oregon Health & Science University)

  • Kevin M. Wright

    (Oregon Health & Science University)

  • Andrew C. Adey

    (Oregon Health & Science University
    Oregon Health & Science University
    CEDAR, Oregon Health & Science University
    Oregon Health & Science University)

Abstract

High-throughput single-cell epigenomic assays can resolve cell type heterogeneity in complex tissues, however, spatial orientation is lost. Here, we present single-cell combinatorial indexing on Microbiopsies Assigned to Positions for the Assay for Transposase Accessible Chromatin, or sciMAP-ATAC, as a method for highly scalable, spatially resolved, single-cell profiling of chromatin states. sciMAP-ATAC produces data of equivalent quality to non-spatial sci-ATAC and retains the positional information of each cell within a 214 micron cubic region, with up to hundreds of tracked positions in a single experiment. We apply sciMAP-ATAC to assess cortical lamination in the adult mouse primary somatosensory cortex and in the human primary visual cortex, where we produce spatial trajectories and integrate our data with non-spatial single-nucleus RNA and other chromatin accessibility single-cell datasets. Finally, we characterize the spatially progressive nature of cerebral ischemic infarction in the mouse brain using a model of transient middle cerebral artery occlusion.

Suggested Citation

  • Casey A. Thornton & Ryan M. Mulqueen & Kristof A. Torkenczy & Andrew Nishida & Eve G. Lowenstein & Andrew J. Fields & Frank J. Steemers & Wenri Zhang & Heather L. McConnell & Randy L. Woltjer & Anusha, 2021. "Spatially mapped single-cell chromatin accessibility," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21515-7
    DOI: 10.1038/s41467-021-21515-7
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    Cited by:

    1. Ruth V. Nichols & Brendan L. O’Connell & Ryan M. Mulqueen & Jerushah Thomas & Ashley R. Woodfin & Sonia Acharya & Gail Mandel & Dmitry Pokholok & Frank J. Steemers & Andrew C. Adey, 2022. "High-throughput robust single-cell DNA methylation profiling with sciMETv2," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

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