A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing.

Abstract:

:Detailed characterization and mapping of oligonucleotide function in vivo is generally a very time consuming effort that only allows for hypothesis driven subsampling of the full sequence to be analysed. Recent advances in deep sequencing together with highly efficient parallel oligonucleotide synthesis and cloning techniques have, however, opened up for entirely new ways to map genetic function in vivo. Here we present a novel, optimized protocol for the generation of universally applicable, barcode labelled, plasmid libraries. The libraries are designed to enable the production of viral vector preparations assessing coding or non-coding RNA function in vivo. When generating high diversity libraries, it is a challenge to achieve efficient cloning, unambiguous barcoding and detailed characterization using low-cost sequencing technologies. With the presented protocol, diversity of above 3 million uniquely barcoded adeno-associated viral (AAV) plasmids can be achieved in a single reaction through a process achievable in any molecular biology laboratory. This approach opens up for a multitude of in vivo assessments from the evaluation of enhancer and promoter regions to the optimization of genome editing. The generated plasmid libraries are also useful for validation of sequencing clustering algorithms and we here validate the newly presented message passing clustering process named Starcode.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Davidsson M,Diaz-Fernandez P,Schwich OD,Torroba M,Wang G,Björklund T

doi

10.1038/srep37563

subject

Has Abstract

pub_date

2016-11-22 00:00:00

pages

37563

issn

2045-2322

pii

srep37563

journal_volume

6

pub_type

杂志文章
  • Absence Seizure Control by a Brain Computer Interface.

    abstract::The ultimate goal of epileptology is the complete abolishment of epileptic seizures. This might be achieved by a system that predicts seizure onset combined with a system that interferes with the process that leads to the onset of a seizure. Seizure prediction remains, as of yet, unresolved in absence-epilepsy, due to...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-02626-y

    authors: Maksimenko VA,van Heukelum S,Makarov VV,Kelderhuis J,Lüttjohann A,Koronovskii AA,Hramov AE,van Luijtelaar G

    更新日期:2017-05-29 00:00:00

  • Numerical Simulation of Hemodynamic Changes in Central Veins after Tunneled Cuffed Central Venous Catheter Placement in Patients under Hemodialysis.

    abstract::The tunneled central venous catheter (CVC) plays an important role for hemodialysis patients, but CVC-related thrombosis in the central veins remain problematic. This study is the first try to numerically find out what hemodynamic parameters are predisposed to the initiation and formation of thrombus after CVC inserti...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-12456-7

    authors: Peng L,Qiu Y,Huang Z,Xia C,Dai C,Zheng T,Li Z

    更新日期:2017-11-21 00:00:00

  • Accumulation of magnetite by flotation on bubbles during decompression of silicate magma.

    abstract::Magnetite (Fe3O4) is an iron ore mineral that is globally mined especially for steel production. It is denser (5.15 g/cm3) than Earth's crust (~2.7 g/cm3) and is expected to accumulate at the bottom of melt-rich magma reservoirs. However, recent studies revealed heterogeneous fluid bubble nucleation on oxide minerals ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-40376-1

    authors: Knipping JL,Webster JD,Simon AC,Holtz F

    更新日期:2019-03-07 00:00:00

  • Regulation of ribonucleotide synthesis by the Pseudomonas aeruginosa two-component system AlgR in response to oxidative stress.

    abstract::Ribonucleotide reductases (RNR) catalyze the last step of deoxyribonucleotide synthesis, and are therefore essential to DNA-based life. Three forms of RNR exist: classes I, II, and III. While eukaryotic cells use only class Ia RNR, bacteria can harbor any combination of classes, granting them adaptability. The opportu...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-17917-7

    authors: Crespo A,Pedraz L,Van Der Hofstadt M,Gomila G,Torrents E

    更新日期:2017-12-20 00:00:00

  • Fabrication of efficient planar perovskite solar cells using a one-step chemical vapor deposition method.

    abstract::Organometallic trihalide perovskites are promising materials for photovoltaic applications, which have demonstrated a rapid rise in photovoltaic performance in a short period of time. We report a facile one-step method to fabricate planar heterojunction perovskite solar cells by chemical vapor deposition (CVD), with a...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep14083

    authors: Tavakoli MM,Gu L,Gao Y,Reckmeier C,He J,Rogach AL,Yao Y,Fan Z

    更新日期:2015-09-22 00:00:00

  • Mitochondrial Genomes of Two Bombycoidea Insects and Implications for Their Phylogeny.

    abstract::The mitochondrial genome (mt genome) provides important information for understanding molecular evolution and phylogenetics. As such, the two complete mt genomes of Ampelophaga rubiginosa and Rondotia menciana were sequenced and annotated. The two circular genomes of A. rubiginosa and R. menciana are 15,282 and 15,636...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-06930-5

    authors: Xin ZZ,Yu Liu,Zhu XY,Wang Y,Zhang HB,Zhang DZ,Zhou CL,Tang BP,Liu QN

    更新日期:2017-07-26 00:00:00

  • Blocking RpoN reduces virulence of Pseudomonas aeruginosa isolated from cystic fibrosis patients and increases antibiotic sensitivity in a laboratory strain.

    abstract::Multidrug-resistant organisms are increasing in healthcare settings, and there are few antimicrobials available to treat infections from these bacteria. Pseudomonas aeruginosa is an opportunistic pathogen in burn patients and individuals with cystic fibrosis (CF), and a leading cause of nosocomial infections. P. aerug...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-43060-6

    authors: Lloyd MG,Vossler JL,Nomura CT,Moffat JF

    更新日期:2019-04-30 00:00:00

  • Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River.

    abstract::Soil microorganisms play a crucial role in the biogeochemical cycling of nutrient elements and maintaining soil health. We aimed to investigate the response of bacteria communities to organic farming over different crops (rice, tea and vegetable) along the middle and lower reaches of the Yangtze River of China. Compar...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep35046

    authors: Wang W,Wang H,Feng Y,Wang L,Xiao X,Xi Y,Luo X,Sun R,Ye X,Huang Y,Zhang Z,Cui Z

    更新日期:2016-10-11 00:00:00

  • Engaging cervical spinal circuitry with non-invasive spinal stimulation and buspirone to restore hand function in chronic motor complete patients.

    abstract::The combined effects of cervical electrical stimulation alone or in combination with the monoaminergic agonist buspirone on upper limb motor function were determined in six subjects with motor complete (AIS B) injury at C5 or above and more than one year from time of injury. Voluntary upper limb function was evaluated...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-33123-5

    authors: Freyvert Y,Yong NA,Morikawa E,Zdunowski S,Sarino ME,Gerasimenko Y,Edgerton VR,Lu DC

    更新日期:2018-10-19 00:00:00

  • A novel function for Egr4 in posterior hindbrain development.

    abstract::Segmentation of the vertebrate hindbrain is an evolutionarily conserved process. Here, we identify the transcription factor early growth response 4 (egr4) as a novel regulator of posterior hindbrain development in Xenopus. egr4 is specifically and transiently expressed in rhombomeres 5 and 6 (r5/r6), and Egr4 knockdow...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep07750

    authors: Bae CJ,Jeong J,Saint-Jeannet JP

    更新日期:2015-01-13 00:00:00

  • Establishment of a guided, in vivo, multi-channel, abdominal, tissue imaging approach.

    abstract::Novel tools in humane animal research should benefit the animal as well as the experimentally obtained data. Imaging technologies have proven to be versatile and also in accordance with the demands of the 3 R principle. However, most imaging technologies are either limited by the target organs, number of repetitive im...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-65950-w

    authors: Bahlmann J,Madrahimov N,Daniel F,Theidel D,DeTemple DE,Buettner M,Bleich A,Haverich A,Heisterkamp A,Kalies S

    更新日期:2020-06-08 00:00:00

  • Fragment-based screening identifies inhibitors of ATPase activity and of hexamer formation of Cagα from the Helicobacter pylori type IV secretion system.

    abstract::Type IV secretion systems are multiprotein complexes that mediate the translocation of macromolecules across the bacterial cell envelope. In Helicobacter pylori a type IV secretion system encoded by the cag pathogenicity island encodes 27 proteins and most are essential for virulence. We here present the identificatio...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-42876-6

    authors: Arya T,Oudouhou F,Casu B,Bessette B,Sygusch J,Baron C

    更新日期:2019-04-24 00:00:00

  • A novel method for identifying and distinguishing Cryptococcus neoformans and Cryptococcus gattii by surface-enhanced Raman scattering using positively charged silver nanoparticles.

    abstract::There are approximately 1 million cryptococcal infections per year among HIV+ individuals, resulting in nearly 625,000 deaths. Cryptococcus neoformans and Cryptococcus gattii are the two most common species that cause human cryptococcosis. These two species of Cryptococcus have differences in pathogenicity, diagnosis,...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-68978-0

    authors: Hu S,Gu F,Chen M,Wang C,Li J,Yang J,Wang G,Zhou Z,Yang Y

    更新日期:2020-07-27 00:00:00

  • Bi-functional IgG-lysosomal enzyme fusion proteins for brain drug delivery.

    abstract::Most lysosomal storage disorders affect the central nervous system. However, lysosomal enzymes do not cross the blood-brain barrier (BBB), and intravenous enzyme infusion is not effective for the brain. Lysosomal enzymes can be re-engineered for BBB transport as IgG-enzyme fusion proteins, where the IgG domain is a mo...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-55136-4

    authors: Boado RJ,Lu JZ,Hui EK,Lin H,Pardridge WM

    更新日期:2019-12-09 00:00:00

  • Natural selection supports escape from concerted evolution of a recently duplicated CEACAM1 paralog in the ruminant CEA gene family.

    abstract::Concerted evolution is often observed in multigene families such as the CEA gene family. As a result, sequence similarity of paralogous genes is significantly higher than expected from their evolutionary distance. Gene conversion, a "copy paste" DNA repair mechanism that transfers sequences from one gene to another an...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-60425-4

    authors: Hänske J,Hammacher T,Grenkowitz F,Mansfeld M,Dau TH,Maksimov P,Friedrich C,Zimmermann W,Kammerer R

    更新日期:2020-02-25 00:00:00

  • The identification of small molecule inhibitors of the plant inositol phosphorylceramide synthase which demonstrate herbicidal activity.

    abstract::Resistance to 157 different herbicides and 88% of known sites of action has been observed, with many weeds resistant to two or more modes. Coupled with tighter environmental regulation, this demonstrates the need to identify new modes of action and novel herbicides. The plant sphingolipid biosynthetic enzyme, inositol...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-44544-1

    authors: Pinneh EC,Mina JG,Stark MJR,Lindell SD,Luemmen P,Knight MR,Steel PG,Denny PW

    更新日期:2019-05-30 00:00:00

  • Author Correction: Localization and function of neurosecretory protein GM, a novel small secretory protein, in the chicken hypothalamus.

    abstract::A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper. ...

    journal_title:Scientific reports

    pub_type: 已发布勘误

    doi:10.1038/s41598-018-24103-w

    authors: Shikano K,Bessho Y,Kato M,Iwakoshi-Ukena E,Taniuchi S,Furumitsu M,Tachibana T,Bentley GE,Kriegsfeld LJ,Ukena K

    更新日期:2018-04-13 00:00:00

  • All muscarinic acetylcholine receptors (M1-M5) are expressed in murine brain microvascular endothelium.

    abstract::Clinical and experimental studies indicate that muscarinic acetylcholine receptors are potential pharmacological targets for the treatment of neurological diseases. Although these receptors have been described in human, bovine and rat cerebral microvascular tissue, a subtype functional characterization in mouse brain ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-05384-z

    authors: Radu BM,Osculati AMM,Suku E,Banciu A,Tsenov G,Merigo F,Di Chio M,Banciu DD,Tognoli C,Kacer P,Giorgetti A,Radu M,Bertini G,Fabene PF

    更新日期:2017-07-11 00:00:00

  • Implication of REDD1 in the activation of inflammatory pathways.

    abstract::In response to endotoxemia, the organism triggers an inflammatory response, and the visceral adipose tissue represents a major source of proinflammatory cytokines. The regulation of inflammation response in the adipose tissue is thus of crucial importance. We demonstrated that Regulated in development and DNA damage r...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-07182-z

    authors: Pastor F,Dumas K,Barthélémy MA,Regazzetti C,Druelle N,Peraldi P,Cormont M,Tanti JF,Giorgetti-Peraldi S

    更新日期:2017-08-01 00:00:00

  • Author Correction: Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1.

    abstract::A correction has been published and is appended to both the HTML and PDF versions of this paper. The error has not been fixed in the paper. ...

    journal_title:Scientific reports

    pub_type: 已发布勘误

    doi:10.1038/s41598-018-37591-7

    authors: Garcia E,Hayden A,Birts C,Britton E,Rogerson C,Bleaney CW,Cowie A,Pickard K,Mellone M,Choh C,Derouet M,Duriez P,Noble F,White MJ,Primrose JN,Strefford JC,Rose-Zerilli M,Thomas GJ,Ang Y,Sharrocks AD,Fitzgerald RC,

    更新日期:2019-01-22 00:00:00

  • Decreased olfactory discrimination is associated with impulsivity in healthy volunteers.

    abstract::In clinical populations, olfactory abilities parallel executive function, implicating shared neuroanatomical substrates within the ventral prefrontal cortex. In healthy individuals, the relationship between olfaction and personality traits or certain cognitive and behavioural characteristics remains unexplored. We the...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-34056-9

    authors: Herman AM,Critchley H,Duka T

    更新日期:2018-10-22 00:00:00

  • Large scale validation of a new non-invasive and non-contact bilirubinometer in neonates with risk factors.

    abstract::The study was aimed to evaluate the performance of a newly developed non-invasive and non-contact bilirubin measurement device (AJO-Neo) as an alternative to the conventional invasive biochemical method of total serum bilirubin (TSB) estimation in preterm and term neonates suffering from hyperbilirubinemia associated ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-67981-9

    authors: Halder A,Adhikari A,Ghosh R,Singh S,Banerjee A,Ghosh N,Bhattacharya AM,Mandal S,Chakrabarti P,Bhattacharyya D,Altass HM,Morad M,Ahmed SA,Mallick AK,Pal SK

    更新日期:2020-07-07 00:00:00

  • Geographical influences on thyroid abnormalities in adult population from iodine-replete regions: a cross-sectional study.

    abstract::The studies on the increasing incidence of thyroid abnormalities are scarce. The aim of this current study was to ascertain the effects of geographical region on thyroid abnormalities under the context of universal salt iodization (USI). We randomly selected 1255 participants residing in inland and 1248 in coast, with...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-80248-7

    authors: Wang X,Mo Z,Mao G,Zhu W,Xing M,Li X,Wang Y,Wang Z,Lou X

    更新日期:2021-01-13 00:00:00

  • Microscale Liquid Transport in Polycrystalline Inverse Opals across Grain Boundaries.

    abstract::Delivering liquid through the void spaces in porous metals is a daunting challenge for a variety of emerging interface technologies ranging from battery electrodes to evaporation surfaces. Hydraulic transport characteristics of well-ordered porous media are governed by the pore distribution, porosity, and morphology. ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-10791-3

    authors: Pham QN,Barako MT,Tice J,Won Y

    更新日期:2017-09-05 00:00:00

  • Revised domain structure of ulvan lyase and characterization of the first ulvan binding domain.

    abstract::Biomass waste products from green algae have recently been given new life, as these polysaccharides have potential applications in industry, agriculture, and medicine. One such polysaccharide group called ulvans displays many different, potentially useful properties that arise from their structural versatility. Hence,...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep44115

    authors: Melcher RL,Neumann M,Fuenzalida Werner JP,Gröhn F,Moerschbacher BM

    更新日期:2017-03-22 00:00:00

  • Cystoid edema, neovascularization and inflammatory processes in the murine Norrin-deficient retina.

    abstract::Mutations in the Norrin (NDP) gene cause severe developmental blood vessel defects in the retina leading to congenital blindness. In the retina of Ndph-knockout mice only the superficial capillary network develops. Here, a detailed characterization of this mouse model at late stages of the disease using in vivo retina...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-24476-y

    authors: Beck SC,Karlstetter M,Garcia Garrido M,Feng Y,Dannhausen K,Mühlfriedel R,Sothilingam V,Seebauer B,Berger W,Hammes HP,Seeliger MW,Langmann T

    更新日期:2018-04-13 00:00:00

  • Characteristics of Cadmium Sorption by Heat-Activated Red Mud in Aqueous Solution.

    abstract::Red mud as a waste material is produced in large quantities by the aluminum industry. Heat activation has been used to enhance sorption capacity of red mud for its beneficial reuse as an effective sorbent. In this study, heat-activated red mud (HARM) was investigated for its Cd(II) sorption capacity under various proc...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-31967-5

    authors: Yang T,Sheng L,Wang Y,Wyckoff KN,He C,He Q

    更新日期:2018-09-10 00:00:00

  • Proton pump inhibitors act synergistically with fluconazole against resistant Candida albicans.

    abstract::The incidence of resistant Candida isolates, especially Candida albicans, has increased continuously. To overcome the resistance, research on antifungal agent sensitizers has attracted considerable attention. Omeprazole and lansoprazole were found to inhibit the growth of sensitive C. albicans and hyphae formation in ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-57174-4

    authors: Lu M,Yan H,Yu C,Yuan L,Sun S

    更新日期:2020-01-16 00:00:00

  • Crystal structures of thiamine monophosphate kinase from Acinetobacter baumannii in complex with substrates and products.

    abstract::Thiamine monophosphate kinase (ThiL) catalyzes the last step of thiamine pyrophosphate (TPP) synthesis, the ATP-dependent phosphorylation of thiamine monophosphate (TMP) to thiamine pyrophosphate. We solved the structure of ThiL from the human pathogen A. baumanii in complex with a pair of substrates TMP and a non-hyd...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-40558-x

    authors: Sullivan AH,Dranow DM,Horanyi PS,Lorimer DD,Edwards TE,Abendroth J

    更新日期:2019-03-13 00:00:00

  • Thioesterase YbgC affects motility by modulating c-di-GMP levels in Shewanella oneidensis.

    abstract::Because of ubiquity of thioesters, thioesterases play a critical role in metabolism, membrane biosynthesis, signal transduction, and gene regulation. In many bacteria, YbgC is such an enzyme, whose coding gene mostly resides in the tol-pal cluster. Although all other proteins encoded in the tol-pal cluster are clearly...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-04285-5

    authors: Gao T,Meng Q,Gao H

    更新日期:2017-06-21 00:00:00