Abstract:
:Droplet single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes. However, assessing differential expression across multiple individuals has been hampered by inefficient sample processing and technical batch effects. Here we describe a computational tool, demuxlet, that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). These capabilities enable multiplexed dscRNA-seq experiments in which cells from unrelated individuals are pooled and captured at higher throughput than in standard workflows. Using simulated data, we show that 50 single-nucleotide polymorphisms (SNPs) per cell are sufficient to assign 97% of singlets and identify 92% of doublets in pools of up to 64 individuals. Given genotyping data for each of eight pooled samples, demuxlet correctly recovers the sample identity of >99% of singlets and identifies doublets at rates consistent with previous estimates. We apply demuxlet to assess cell-type-specific changes in gene expression in 8 pooled lupus patient samples treated with interferon (IFN)-β and perform eQTL analysis on 23 pooled samples.
journal_name
Nat Biotechnoljournal_title
Nature biotechnologyauthors
Kang HM,Subramaniam M,Targ S,Nguyen M,Maliskova L,McCarthy E,Wan E,Wong S,Byrnes L,Lanata CM,Gate RE,Mostafavi S,Marson A,Zaitlen N,Criswell LA,Ye CJdoi
10.1038/nbt.4042subject
Has Abstractpub_date
2018-01-01 00:00:00pages
89-94issue
1eissn
1087-0156issn
1546-1696pii
nbt.4042journal_volume
36pub_type
杂志文章abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...
journal_title:Nature biotechnology
pub_type: 已发布勘误
doi:10.1038/s41587-019-0253-5
更新日期:2019-09-01 00:00:00
abstract::The efficiency of both phage display in Escherichia coli and periplasmic expression of recombinant proteins may be limited by the same periplasmic folding steps. To search for E. coli factors that improve the efficiency of both procedures, a library of E. coli proteins was coexpressed in a phagemid vector that contain...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt0498-376
更新日期:1998-04-01 00:00:00
abstract::Genome editing with targeted nucleases and DNA donor templates homologous to the break site has proven challenging in human hematopoietic stem and progenitor cells (HSPCs), and particularly in the most primitive, long-term repopulating cell population. Here we report that combining electroporation of zinc finger nucle...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3408
更新日期:2015-12-01 00:00:00
abstract::The green fluorescent protein (GFP) from the jellyfish Aequorea victoria and its fluorescent homologs from Anthozoa corals have become invaluable tools for in vivo imaging of cells and tissues. Despite spectral and chromophore diversity, about 100 cloned members of the GFP-like protein family possess common structural...
journal_title:Nature biotechnology
pub_type: 杂志文章,评审
doi:10.1038/nbt943
更新日期:2004-03-01 00:00:00
abstract::The application of single-cell genome sequencing to large cell populations has been hindered by technical challenges in isolating single cells during genome preparation. Here we present single-cell genomic sequencing (SiC-seq), which uses droplet microfluidics to isolate, fragment, and barcode the genomes of single ce...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3880
更新日期:2017-07-01 00:00:00
abstract::Expansions of short tandem repeats are genetic variants that have been implicated in several neuropsychiatric and other disorders, but their assessment remains challenging with current polymerase-based methods1-4. Here we introduce a CRISPR-Cas-based enrichment strategy for nanopore sequencing combined with an algorit...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/s41587-019-0293-x
更新日期:2019-12-01 00:00:00
abstract::Understanding how proteins and their complex interaction networks convert the genomic information into a dynamic living organism is a fundamental challenge in biological sciences. As an important step towards understanding the systems biology of a complex eukaryote, we cataloged 63% of the predicted Drosophila melanog...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1300
更新日期:2007-05-01 00:00:00
abstract::The discovery of large multiprotein complexes in cells has increased the demand for improved heterologous protein production techniques to study their molecular structure and function. Here we describe MultiBac, a simple and versatile system for generating recombinant baculovirus DNA to express protein complexes compr...
journal_title:Nature biotechnology
pub_type: 信件
doi:10.1038/nbt1036
更新日期:2004-12-01 00:00:00
abstract::We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparativ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3886
更新日期:2017-07-01 00:00:00
abstract::New cultivars with very erect leaves, which increase light capture for photosynthesis and nitrogen storage for grain filling, may have increased grain yields. Here we show that the erect leaf phenotype of a rice brassinosteroid-deficient mutant, osdwarf4-1, is associated with enhanced grain yields under conditions of ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1173
更新日期:2006-01-01 00:00:00
abstract::This report describes the selection of highly efficient antibody catalysts by combining chemical selection from a synthetic library with directed in vitro protein evolution. Evolution started from a naive antibody library displayed on phage made from fully synthetic, antibody-encoding genes (the Human Combinatorial An...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt828
更新日期:2003-06-01 00:00:00
abstract::The expression patterns of eukaryotic genomes are controlled by their chromatin structure, consisting of nucleosome subunits in which DNA of approximately 146 bp is wrapped around a core of 8 histone molecules. Post-translational histone modifications play an essential role in modifying chromatin structure. Here we ap...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt990
更新日期:2004-08-01 00:00:00
abstract::Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C(4) biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (∼423 Mb) anchored onto nine chrom...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.2195
更新日期:2012-05-13 00:00:00
abstract::Purging of tumor cells and selection of stem cells are key technologies for enabling stem cell transplantation and stem cell gene therapy. Here we report a strategy for cell selection based on physical properties of the cells. Exposing cells to an external pulsed electric field (PEF) increases the natural potential di...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/78504
更新日期:2000-08-01 00:00:00
abstract::Small-interfering RNAs (siRNAs) assemble into RISC, the RNA-induced silencing complex, which cleaves complementary mRNAs. Despite their fluctuating efficacy, siRNAs are widely used to assess gene function. Although this limitation could be ascribed, in part, to variations in the assembly and activation of RISC, downst...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1404
更新日期:2008-05-01 00:00:00
abstract::The use of DNA variants in the mapping of the human genome and in the positional cloning of monogenic disease genes is well established. Determining the genetic bases of the more common "multifactorial" diseases, however, presents a major challenge. The genetics of these diseases are complicated by the interplay betwe...
journal_title:Nature biotechnology
pub_type: 杂志文章,评审
doi:10.1038/nbt0198-33
更新日期:1998-01-01 00:00:00
abstract::A problem in analyzing microarray-based gene expression data is the separation of genes causally involved in a disease from innocent bystander genes, whose expression levels have been secondarily altered by primary changes elsewhere. To investigate this issue systematically in the context of a class of complex human d...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt965
更新日期:2004-05-01 00:00:00
abstract::Recent therapeutic successes have renewed interest in drug combinations, but experimental screening approaches are costly and often identify only small numbers of synergistic combinations. The DREAM consortium launched an open challenge to foster the development of in silico methods to computationally rank 91 compound...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3052
更新日期:2014-12-01 00:00:00
abstract::Nucleotide variants, especially those related to epigenetic functions, provide critical regulatory information beyond simple genomic sequence, and they define cell status in higher organisms. 5-Methylcytosine, which is found in DNA, was until recently the only nucleotide variant studied in terms of epigenetics in euka...
journal_title:Nature biotechnology
pub_type: 杂志文章,评审
doi:10.1038/nbt.2398
更新日期:2012-11-01 00:00:00
abstract::We have developed novel nucleic acid probes that recognize and report the presence of specific nucleic acids in homogeneous solutions. These probes undergo a spontaneous fluorogenic conformational change when they hybridize to their targets. Only perfectly complementary targets elicit this response, as hybridization d...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt0396-303
更新日期:1996-03-01 00:00:00
abstract::Cellular function is critically regulated through degradation of substrates by the proteasome. To enable direct analysis of naturally cleaved proteasomal peptides under physiological conditions, we developed mass spectrometry analysis of proteolytic peptides (MAPP), a method for proteasomal footprinting that allows fo...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.4279
更新日期:2018-10-22 00:00:00
abstract::The targeting scope of Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants is largely restricted to protospacer-adjacent motif (PAM) sequences containing G bases. Here we report the evolution of three new SpCas9 variants that collectively recognize NRNH PAMs (where R is A or G and H is A, C or T) using ph...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/s41587-020-0412-8
更新日期:2020-04-01 00:00:00
abstract::Current base editors (BEs) catalyze only base transitions (C to T and A to G) and cannot produce base transversions. Here we present BEs that cause C-to-A transversions in Escherichia coli and C-to-G transversions in mammalian cells. These glycosylase base editors (GBEs) consist of a Cas9 nickase, a cytidine deaminase...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/s41587-020-0592-2
更新日期:2021-01-01 00:00:00
abstract::Protein phosphorylation is a dominant mechanism of information transfer in cells, and a major goal of current proteomic efforts is to generate a system-level map describing all the sites of protein phosphorylation. Recent efforts have focused on developing technologies for enriching and quantifying phosphopeptides. Id...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt863
更新日期:2003-09-01 00:00:00
abstract::De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable rapid human genome assembly, we present Shasta, a de novo long-read assembler, and polishing algorithms named MarginPolish and HELEN. Using a single P...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/s41587-020-0503-6
更新日期:2020-09-01 00:00:00
abstract::Mice repopulated with human hematopoietic cells are a powerful tool for the study of human hematopoiesis and immune function in vivo. However, existing humanized mouse models cannot support development of human innate immune cells, including myeloid cells and natural killer (NK) cells. Here we describe two mouse strai...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.2858
更新日期:2014-04-01 00:00:00
abstract::Fewer than half of all tandem mass spectrometry (MS/MS) spectra acquired in shotgun proteomics experiments are typically matched to a peptide with high confidence. Here we determine the identity of unassigned peptides using an ultra-tolerant Sequest database search that allows peptide matching even with modifications ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3267
更新日期:2015-07-01 00:00:00
abstract::Phosphorus (P) is one of the most important nutrients limiting agricultural production worldwide. In acid and alkaline soils, which make up over 70% of the world's arable land, P forms insoluble compounds that are not available for plant use. To reduce P deficiencies and ensure plant productivity, nearly 30 million to...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/74531
更新日期:2000-04-01 00:00:00
abstract::Lipid production in the industrial microalga Nannochloropsis gaditana exceeds that of model algal species and can be maximized by nutrient starvation in batch culture. However, starvation halts growth, thereby decreasing productivity. Efforts to engineer N. gaditana strains that can accumulate biomass and overproduce ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt.3865
更新日期:2017-07-01 00:00:00
abstract::Efficiently generating evidence of clinical utility is a major challenge for ensuring clinical adoption of valuable diagnostics. A new approach to reimbursement in the United States offers a balance between evidence and incentives for molecular diagnostic tests. ...
journal_title:Nature biotechnology
pub_type: 杂志文章
doi:10.1038/nbt1110-1157
更新日期:2010-11-01 00:00:00