13
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: not found
      • Article: not found

      Three-dimensional intact-tissue sequencing of single-cell transcriptional states

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Retrieving high-content gene-expression information while retaining 3D positional anatomy at cellular resolution has been difficult, limiting integrative understanding of structure and function in complex biological tissues. Here we develop and apply a technology for 3D intact-tissue RNA sequencing, termed STARmap (Spatially-resolved Transcript Amplicon Readout Mapping), which integrates hydrogel-tissue chemistry, targeted signal amplification, and in situ sequencing. The capabilities of STARmap were tested by mapping 160 to 1,020 genes simultaneously in sections of mouse brain at single-cell resolution with high efficiency, accuracy and reproducibility. Moving to thick tissue blocks, we observed a molecularly-defined gradient distribution of excitatory-neuron subtypes across cubic millimeter-scale volumes (>30,000 cells), and discovered a short-range 3D self-clustering in many inhibitory-neuron subtypes that could be identified and described with 3D STARmap.

          Related collections

          Most cited references24

          • Record: found
          • Abstract: not found
          • Article: not found

          Hydrogels in Biology and Medicine: From Molecular Principles to Bionanotechnology

            Bookmark
            • Record: found
            • Abstract: not found
            • Article: not found

            Multidimensional binary search trees used for associative searching

              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Accurate multiplex polony sequencing of an evolved bacterial genome.

              We describe a DNA sequencing technology in which a commonly available, inexpensive epifluorescence microscope is converted to rapid nonelectrophoretic DNA sequencing automation. We apply this technology to resequence an evolved strain of Escherichia coli at less than one error per million consensus bases. A cell-free, mate-paired library provided single DNA molecules that were amplified in parallel to 1-micrometer beads by emulsion polymerase chain reaction. Millions of beads were immobilized in a polyacrylamide gel and subjected to automated cycles of sequencing by ligation and four-color imaging. Cost per base was roughly one-ninth as much as that of conventional sequencing. Our protocols were implemented with off-the-shelf instrumentation and reagents.
                Bookmark

                Author and article information

                Journal
                Science
                Science
                American Association for the Advancement of Science (AAAS)
                0036-8075
                1095-9203
                July 26 2018
                July 27 2018
                July 27 2018
                June 21 2018
                : 361
                : 6400
                : eaat5691
                Article
                10.1126/science.aat5691
                6339868
                29930089
                88db7884-2161-4bf9-90ab-8afec64e4471
                © 2018

                http://www.sciencemag.org/about/science-licenses-journal-article-reuse


                Comments

                Comment on this article