Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells
Open accessAbstract
Genome sequencing of single cells has a variety of applications, including characterizing difficult-to-culture microorganisms and identifying somatic mutations in single cells from mammalian tissues. A major hurdle in this process is the bias in amplifying the genetic material from a single cell, a procedure known as polymerase cloning. Here we describe the microwell displacement amplification system (MIDAS), a massively parallel polymerase cloning method in which single cells are randomly distributed into hundreds to thousands of nanoliter wells and their genetic material is simultaneously amplified for shotgun sequencing. MIDAS reduces amplification bias because polymerase cloning occurs in physically separated, nanoliter-scale reactors, facilitating the de novo assembly of near-complete microbial genomes from single Escherichia coli cells. In addition, MIDAS allowed us to detect single-copy number changes in primary human adult neurons at 1- to 2-Mb resolution. MIDAS can potentially further the characterization of genomic diversity in many heterogeneous cell populations.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Early successes include parallel measurement of the transcriptome and either the genome (DR-seq and G&T-seq), the methylome (scM&T-seq, an adaptation of G&T-seq), or the proteome.
“Early successes include parallel measurement of the transcriptome and either the genome (DR-seq209 and G&T-seq210), the methylome (scM&T-seq211, an adaptation of G&T-seq), or the proteome212–214.”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [210]
Emerging experimental frameworks now allow simultaneous measurement of multiple omic data types from the same single cell.
“Emerging experimental frameworks now allow simultaneous measurement of multiple omic data types from the same single cell.”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [210]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
The citation lists haven’t been fetched yet
References 41 · Cited by 238
- Authors
- Gole, J., Gore, A., Richards, A., Chiu, Y.-J., Fung, H.-L., Bushman, D., Chiang, H.-I., Chun, J., Lo, Y.-H., & Zhang, K.
- Affiliations
- University of California San Diego (US)
- Scripps Research Institute (US)
- National Chung Hsing University (TW)
- Corresponding author
- Zhang, Kun
- Venue
- Nature Biotechnology
- Published
- 2013-12
- Volume
- 31
- Issue
- 12
- Pages
- 1126-1132
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC3875318
- OpenAlex
- W2111747321
- Cited by
- 238
- References
- 41
- Citations by year
- 2026: 2 · 2025: 4 · 2024: 9 · 2023: 13 · 2022: 14 · 2021: 14 · 2020: 21 · 2019: 20 · 2018: 35 · 2017: 28 · 2016: 21 · 2015: 30 · 2014: 26 · 2013: 1
- FWCI
- 11.65
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation
- National Institutes of Health
- University of California, San Diego
- National Institute of Mental Health (U01MH098977)
- National Human Genome Research Institute (P50HG005550, R01HG004876)
- National Institute of General Medical Sciences (T32GM007752, R01GM097253)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- single-cell DNA sequencing, MIDAS, amplification bias, shotgun sequencing, de novo genome assembly, Escherichia coli, somatic mutations, microbial genomics
- MeSH terms
- Cell Separation, Chromosome Mapping, Cloning, Molecular, DNA, DNA-Directed DNA Polymerase, Equipment Design, Equipment Failure Analysis, Nanotechnology, High-Throughput Nucleotide Sequencing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
