当前位置： SCI文献检索 > NATURE BIOTECHNOLOGY期刊下所有文献 > Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding.

Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding.

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 cells, followed by Illumina sequencing of pooled DNA. We demonstrate ultra-high-throughput sequencing of >50,000 cells per run in a synthetic community of Gram-negative and Gram-positive bacteria and fungi. The sequenced genomes can be sorted in silico based on characteristic sequences. We use this approach to analyze the distributions of antibiotic-resistance genes, virulence factors, and phage sequences in microbial communities from an environmental sample. The ability to routinely sequence large populations of single cells will enable the de-convolution of genetic heterogeneity in diverse cell populations.

journal_name

Nat Biotechnol

journal_title

Nature biotechnology

authors

Lan F,Demaree B,Ahmed N,Abate AR

doi

10.1038/nbt.3880

subject

Has Abstract

pub_date

2017-07-01 00:00:00

pages

640-646

issue

7

eissn

1087-0156

issn

1546-1696

pii

nbt.3880

journal_volume

35

pub_type

杂志文章

相关文献

NATURE BIOTECHNOLOGY文献大全
  • Statistical pattern matching facilitates the design of polyvalent inhibitors of anthrax and cholera toxins.

    abstract：:Numerous biological processes involve the recognition of a specific pattern of binding sites on a target protein or surface. Although ligands displayed by disordered scaffolds form stochastic rather than specific patterns, theoretical models predict that recognition will occur between patterns that are characterized b...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt1204

    authors： Rai P,Padala C,Poon V,Saraph A,Basha S,Kate S,Tao K,Mogridge J,Kane RS

    更新日期：2006-05-01 00:00:00

  • RNA processing enables predictable programming of gene expression.

    abstract：:Complex interactions among genetic components often result in variable systemic performance in designed multigene systems. Using the bacterial clustered regularly interspaced short palindromic repeat (CRISPR) pathway we develop a synthetic RNA-processing platform, and show that efficient and specific cleavage of precu...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.2355

    authors： Qi L,Haurwitz RE,Shao W,Doudna JA,Arkin AP

    更新日期：2012-10-01 00:00:00

  • Improved properties of FLP recombinase evolved by cycling mutagenesis.

    abstract：:The site-specific recombinases FLP and Cre are useful for genomic engineering in many living systems. Manipulation of their enzymatic properties offers a means to improve their applicability in different host organisms. We chose to manipulate the thermolability of FLP recombinase. A lacZ-based recombination assay in E...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt0798-657

    authors： Buchholz F,Angrand PO,Stewart AF

    更新日期：1998-07-01 00:00:00

  • Author Correction: Plants with genetically encoded autoluminescence.

    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/s41587-020-0578-0

    authors： Mitiouchkina T,Mishin AS,Somermeyer LG,Markina NM,Chepurnyh TV,Guglya EB,Karataeva TA,Palkina KA,Shakhova ES,Fakhranurova LI,Chekova SV,Tsarkova AS,Golubev YV,Negrebetsky VV,Dolgushin SA,Shalaev PV,Shlykov D,Melnik OA,

    更新日期：2020-08-01 00:00:00

  • The pharmacological basis of anti-IgE therapy.

    abstract：:The treatment of asthma and allergic rhinitis using unique, humanized anti-IgE monoclonal antibodies with very particular binding specificities is now supported by the results of multiple phase II and III human clinical studies. The therapeutic efficacy of this approach is attributable to several pharmacological mecha...

    journal_title：Nature biotechnology

    pub_type： 杂志文章,评审

    doi：10.1038/72601

    authors： Chang TW

    更新日期：2000-02-01 00:00:00

  • Insecticidal proteins from Bacillus thuringiensis protect corn from corn rootworms.

    abstract：:Field tests of corn co-expressing two new delta-endotoxins from Bacillus thuringiensis (Bt) have demonstrated protection from root damage by western corn rootworm (Diabrotica virgifera virgifera LeConte). The level of protection exceeds that provided by chemical insecticides. In the bacterium, these proteins form crys...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/90282

    authors： Moellenbeck DJ,Peters ML,Bing JW,Rouse JR,Higgins LS,Sims L,Nevshemal T,Marshall L,Ellis RT,Bystrak PG,Lang BA,Stewart JL,Kouba K,Sondag V,Gustafson V,Nour K,Xu D,Swenson J,Zhang J,Czapla T,Schwab G,Jayne S,St

    更新日期：2001-07-01 00:00:00

  • The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

    abstract：:The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthe...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.2891

    authors： Galdzicki M,Clancy KP,Oberortner E,Pocock M,Quinn JY,Rodriguez CA,Roehner N,Wilson ML,Adam L,Anderson JC,Bartley BA,Beal J,Chandran D,Chen J,Densmore D,Endy D,Grünberg R,Hallinan J,Hillson NJ,Johnson JD,Kuchinsky

    更新日期：2014-06-01 00:00:00

  • Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain.

    abstract：:Recombinant adeno-associated viruses (rAAVs) are commonly used vehicles for in vivo gene transfer. However, the tropism repertoire of naturally occurring AAVs is limited, prompting a search for novel AAV capsids with desired characteristics. Here we describe a capsid selection method, called Cre recombination-based AA...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.3440

    authors： Deverman BE,Pravdo PL,Simpson BP,Kumar SR,Chan KY,Banerjee A,Wu WL,Yang B,Huber N,Pasca SP,Gradinaru V

    更新日期：2016-02-01 00:00:00

  • A signal sequence trap based on a constitutively active cytokine receptor.

    abstract：:Targeting of secreted and cell-surface proteins to the cell membrane is mediated by a short hydrophobic stretch of amino acids, termed the signal sequence. We have developed a method that detects signal sequences in cDNA fragments based on their ability to redirect a constitutively active mutant of a cytokine receptor...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/8666

    authors： Kojima T,Kitamura T

    更新日期：1999-05-01 00:00:00

  • A community computational challenge to predict the activity of pairs of compounds.

    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

    authors： Bansal M,Yang J,Karan C,Menden MP,Costello JC,Tang H,Xiao G,Li Y,Allen J,Zhong R,Chen B,Kim M,Wang T,Heiser LM,Realubit R,Mattioli M,Alvarez MJ,Shen Y,NCI-DREAM Community.,Gallahan D,Singer D,Saez-Rodriguez J,

    更新日期：2014-12-01 00:00:00

  • Visualizing lipid-formulated siRNA release from endosomes and target gene knockdown.

    abstract：:A central hurdle in developing small interfering RNAs (siRNAs) as therapeutics is the inefficiency of their delivery across the plasma and endosomal membranes to the cytosol, where they interact with the RNA interference machinery. With the aim of improving endosomal release, a poorly understood and inefficient proces...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.3298

    authors： Wittrup A,Ai A,Liu X,Hamar P,Trifonova R,Charisse K,Manoharan M,Kirchhausen T,Lieberman J

    更新日期：2015-08-01 00:00:00

  • Low-temperature resistance of higher plants is significantly enhanced by a nonspecific cyanobacterial desaturase.

    abstract：:A broad-specificity delta 9 desaturase gene was cloned from the cyanobacterium Anacystis nidulans. The enzyme introduces a cis-double bond at the delta 9 position of both 16 and 18 carbon saturated fatty acids linked to many kinds of membrane lipids. The gene was stably introduced into tobacco plants under transcripti...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt0896-1003

    authors： Ishizaki-Nishizawa O,Fujii T,Azuma M,Sekiguchi K,Murata N,Ohtani T,Toguri T

    更新日期：1996-08-01 00:00:00

  • Presymptomatic visualization of plant-virus interactions by thermography.

    abstract：:Salicylic acid (SA), produced by plants as a signal in defense against pathogens, induces metabolic heating mediated by alternative respiration in flowers of thermogenic plants, and, when exogenously applied, increases leaf temperature in nonthermogenic plants. We have postulated that the latter phenomenon would be de...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/11765

    authors： Chaerle L,Van Caeneghem W,Messens E,Lambers H,Van Montagu M,Van Der Straeten D

    更新日期：1999-08-01 00:00:00

  • Molecular beacons: probes that fluoresce upon hybridization.

    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

    authors： Tyagi S,Kramer FR

    更新日期：1996-03-01 00:00:00

  • Publisher Correction: Death by inflammation: drug makers chase the master controller.

    abstract：:In the version of this article initially published, a GlaxoSmithKline compound referred to as GSK298559 was listed in Table 1 as a RIPK1 inhibitor in phase 1 trials for inflammatory bowel disease. The correct designation is GSK2983559; however, this compound is a RIPK2 inhibitor and thus should not have been included ...

    journal_title：Nature biotechnology

    pub_type： 杂志文章,已发布勘误

    doi：10.1038/s41587-019-0082-6

    authors： Sheridan C

    更新日期：2019-04-01 00:00:00

  • Publisher Correction: OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data.

    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： 杂志文章,已发布勘误

    doi：10.1038/s41587-020-0457-8

    authors： Röst HL,Rosenberger G,Navarro P,Gillet L,Miladinović SM,Schubert OT,Wolski W,Collins BC,Malmström J,Malmström L,Aebersold R

    更新日期：2020-03-01 00:00:00

  • Identification of a cyclohexylcarbonyl CoA biosynthetic gene cluster and application in the production of doramectin.

    abstract：:The side chain of the antifungal antibiotic ansatrienin A from Streptomyces collinus contains a cyclohexanecarboxylic acid (CHC)-derived moiety. This moiety is also observed in trace amounts of omega-cyclohexyl fatty acids (typically less than 1% of total fatty acids) produced by S. collinus. Coenzyme A-activated CHC ...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/79479

    authors： Cropp TA,Wilson DJ,Reynolds KA

    更新日期：2000-09-01 00:00:00

  • Using virally expressed melanoma cDNA libraries to identify tumor-associated antigens that cure melanoma.

    abstract：:Multiple intravenous injections of a cDNA library, derived from human melanoma cell lines and expressed using the highly immunogenic vector vesicular stomatitis virus (VSV), cured mice with established melanoma tumors. Successful tumor eradication was associated with the ability of mouse lymphoid cells to mount a tumo...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.2157

    authors： Pulido J,Kottke T,Thompson J,Galivo F,Wongthida P,Diaz RM,Rommelfanger D,Ilett E,Pease L,Pandha H,Harrington K,Selby P,Melcher A,Vile R

    更新日期：2012-03-18 00:00:00

  • Excision of selectable marker genes from transgenic plants.

    abstract：:Selectable marker genes are required to ensure the efficient genetic modification of crops. Economic incentives and safety concerns have prompted the development of several strategies (site-specific recombination, homologous recombination, transposition, and co-transformation) to eliminate these genes from the genome ...

    journal_title：Nature biotechnology

    pub_type： 杂志文章,评审

    doi：10.1038/nbt0602-575

    authors： Hare PD,Chua NH

    更新日期：2002-06-01 00:00:00

  • A dual-constriction biological nanopore resolves homonucleotide sequences with high fidelity.

    abstract：:Single-molecule long-read DNA sequencing with biological nanopores is fast and high-throughput but suffers reduced accuracy in homonucleotide stretches. We now combine the CsgG nanopore with the 35-residue N-terminal region of its extracellular interaction partner CsgF to produce a dual-constriction pore with improved...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/s41587-020-0570-8

    authors： Van der Verren SE,Van Gerven N,Jonckheere W,Hambley R,Singh P,Kilgour J,Jordan M,Wallace EJ,Jayasinghe L,Remaut H

    更新日期：2020-12-01 00:00:00

  • Growth factors regulate the survival and fate of cells derived from human neurospheres.

    abstract：:Cells isolated from the embryonic, neonatal, and adult rodent central nervous system divide in response to epidermal growth factor (EGF) and fibroblast growth factor 2 (FGF-2), while retaining the ability to differentiate into neurons and glia. These cultures can be grown in aggregates termed neurospheres, which conta...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/88158

    authors： Caldwell MA,He X,Wilkie N,Pollack S,Marshall G,Wafford KA,Svendsen CN

    更新日期：2001-05-01 00:00:00

  • Prospects for plant-derived antibacterials.

    abstract：:Can weakly active phytochemicals be combined synergistically to produce new antibacterial treatments? ...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt1206-1504

    authors： Lewis K,Ausubel FM

    更新日期：2006-12-01 00:00:00

  • Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation.

    abstract：:Whole-genome mRNA quantitation can be used to identify the genes that are most responsive to environmental or genotypic change. By searching for mutually similar DNA elements among the upstream non-coding DNA sequences of these genes, we can identify candidate regulatory motifs and corresponding candidate sets of core...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt1098-939

    authors： Roth FP,Hughes JD,Estep PW,Church GM

    更新日期：1998-10-01 00:00:00

  • Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape.

    abstract：:We describe protein interaction quantitation (PIQ), a computational method for modeling the magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify transcription factor (TF) binding sites. Through the use of machine-learning techniques, PIQ identified binding sites for >700 TFs from one DNase ...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.2798

    authors： Sherwood RI,Hashimoto T,O'Donnell CW,Lewis S,Barkal AA,van Hoff JP,Karun V,Jaakkola T,Gifford DK

    更新日期：2014-02-01 00:00:00

  • Tandem fluorescent protein timers for in vivo analysis of protein dynamics.

    abstract：:The functional state of a cell is largely determined by the spatiotemporal organization of its proteome. Technologies exist for measuring particular aspects of protein turnover and localization, but comprehensive analysis of protein dynamics across different scales is possible only by combining several methods. Here w...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.2281

    authors： Khmelinskii A,Keller PJ,Bartosik A,Meurer M,Barry JD,Mardin BR,Kaufmann A,Trautmann S,Wachsmuth M,Pereira G,Huber W,Schiebel E,Knop M

    更新日期：2012-06-24 00:00:00

  • Data storage in DNA with fewer synthesis cycles using composite DNA letters.

    abstract：:The density and long-term stability of DNA make it an appealing storage medium, particularly for long-term data archiving. Existing DNA storage technologies involve the synthesis and sequencing of multiple nominally identical molecules in parallel, resulting in information redundancy. We report the development of enco...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/s41587-019-0240-x

    authors： Anavy L,Vaknin I,Atar O,Amit R,Yakhini Z

    更新日期：2019-10-01 00:00:00

  • Development and function of human innate immune cells in a humanized mouse model.

    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

    authors： Rongvaux A,Willinger T,Martinek J,Strowig T,Gearty SV,Teichmann LL,Saito Y,Marches F,Halene S,Palucka AK,Manz MG,Flavell RA

    更新日期：2014-04-01 00:00:00

  • Deep learning improves prediction of CRISPR-Cpf1 guide RNA activity.

    abstract：:We present two algorithms to predict the activity of AsCpf1 guide RNAs. Indel frequencies for 15,000 target sequences were used in a deep-learning framework based on a convolutional neural network to train Seq-deepCpf1. We then incorporated chromatin accessibility information to create the better-performing DeepCpf1 a...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.4061

    authors： Kim HK,Min S,Song M,Jung S,Choi JW,Kim Y,Lee S,Yoon S,Kim HH

    更新日期：2018-03-01 00:00:00

  • StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.

    abstract：:Methods used to sequence the transcriptome often produce more than 200 million short sequences. We introduce StringTie, a computational method that applies a network flow algorithm originally developed in optimization theory, together with optional de novo assembly, to assemble these complex data sets into transcripts...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.3122

    authors： Pertea M,Pertea GM,Antonescu CM,Chang TC,Mendell JT,Salzberg SL

    更新日期：2015-03-01 00:00:00

  • Large multiple sequence alignments with a root-to-leaf regressive method.

    abstract：:Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorpora...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/s41587-019-0333-6

    authors： Garriga E,Di Tommaso P,Magis C,Erb I,Mansouri L,Baltzis A,Laayouni H,Kondrashov F,Floden E,Notredame C

    更新日期：2019-12-01 00:00:00