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High-content single-cell combinatorial indexing.
| Content Provider | Europe PMC |
|---|---|
| Author | Mulqueen, Ryan M. Pokholok, Dmitry O’Connell, Brendan L. Thornton, Casey A. Zhang, Fan O’Roak, Brian J. Link, Jason Yardımcı, Galip Gürkan Sears, Rosalie C. Steemers, Frank J. Adey, Andrew C. |
| Abstract | Single-cell combinatorial indexing (sci) with transposase-based library construction increases the throughput of single-cell genomics assays but produces sparse coverage in terms of usable reads per cell. We develop symmetrical strand sci (‘s3’), a uracil-based adapter switching approach that improves the rate of conversion of source DNA into viable sequencing library fragments following tagmentation. We apply this chemistry to assay chromatin accessibility (s3-ATAC) in human cortical and mouse whole brain tissues, with mouse datasets demonstrating a 6-to-13-fold improvement in usable reads per cell compared with other available methods. Application of s3 to single-cell whole genome sequencing (s3-WGS) and to whole genome plus chromatin conformation (s3-GCC) yields 148 and 14.8 fold improvements, respectively, in usable reads per cell compared with sci-DNA-seq and sci-HiC. We show that s3-WGS and s3-GCC resolve subclonal genomic alterations in patient-derived pancreatic cancer cell lines. We expect that the s3 platform will be compatible with other transposase-based techniques, including sci-MET or CUT&Tag. |
| Related Links | https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC8678206&blobtype=pdf |
| ISSN | 10870156 |
| Journal | Nature biotechnology [Nat Biotechnol] |
| Volume Number | 39 |
| DOI | 10.1038/s41587-021-00962-z |
| PubMed Central reference number | PMC8678206 |
| Issue Number | 12 |
| PubMed reference number | 34226710 |
| e-ISSN | 15461696 |
| Language | English |
| Publisher Date | 2021-07-05 |
| Access Restriction | Open |
| Rights License | Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms |
| Content Type | Text |
| Resource Type | Article |
| Subject | Molecular Medicine Bioengineering Biomedical Engineering Applied Microbiology and Biotechnology Biotechnology |
