当前位置： SCI文献检索 > Scientific Reports期刊下所有文献 > PrimerSuite: A High-Throughput Web-Based Primer Design Program for Multiplex Bisulfite PCR.

PrimerSuite: A High-Throughput Web-Based Primer Design Program for Multiplex Bisulfite PCR.

Abstract：

:The analysis of DNA methylation at CpG dinucleotides has become a major research focus due to its regulatory role in numerous biological processes, but the requisite need for assays which amplify bisulfite-converted DNA represents a major bottleneck due to the unique design constraints imposed on bisulfite-PCR primers. Moreover, a review of the literature indicated no available software solutions which accommodated both high-throughput primer design, support for multiplex amplification assays, and primer-dimer prediction. In response, the tri-modular software package PrimerSuite was developed to support bisulfite multiplex PCR applications. This software was constructed to (i) design bisulfite primers against multiple regions simultaneously (PrimerSuite), (ii) screen for primer-primer dimerizing artefacts (PrimerDimer), and (iii) support multiplex PCR assays (PrimerPlex). Moreover, a major focus in the development of this software package was the emphasis on extensive empirical validation, and over 1300 unique primer pairs have been successfully designed and screened, with over 94% of them producing amplicons of the expected size, and an average mapping efficiency of 93% when screened using bisulfite multiplex resequencing. The potential use of the software in other bisulfite-based applications such as methylation-specific PCR is under consideration for future updates. This resource is freely available for use at PrimerSuite website (www.primer-suite.com).

journal_name

Sci Rep

journal_title

Scientific reports

authors

Lu J,Johnston A,Berichon P,Ru KL,Korbie D,Trau M

doi

10.1038/srep41328

subject

Has Abstract

pub_date

2017-01-24 00:00:00

pages

41328

issn

2045-2322

pii

srep41328

journal_volume

7

pub_type

杂志文章

相关文献

Scientific Reports文献大全
  • Reactive saccade adaptation boosts orienting of visuospatial attention.

    abstract：:Attention and saccadic eye movements are critical components of visual perception. Recent studies proposed the hypothesis of a tight coupling between saccadic adaptation (SA) and attention: SA increases the processing speed of unpredictable stimuli, while increased attentional load boosts SA. Moreover, their cortical ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-70120-z

    authors： Nicolas J,Bidet-Caulet A,Pélisson D

    更新日期：2020-08-10 00:00:00

  • Enhancement of human sodium iodide symporter gene therapy for breast cancer by HDAC inhibitor mediated transcriptional modulation.

    abstract：:The aberrant expression of human sodium iodide symporter (NIS) in breast cancer (BC) has raised the possibility of using targeted radioiodide therapy. Here we investigate modulation of endogenous, functional NIS expression by histone deacetylase inhibitors (HDACi) in vitro and in vivo. Luciferase reporter based initia...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep19341

    authors： Kelkar MG,Senthilkumar K,Jadhav S,Gupta S,Ahn BC,De A

    更新日期：2016-01-18 00:00:00

  • The effect of silencing 20E biosynthesis relative genes by feeding bacterially expressed dsRNA on the larval development of Chilo suppressalis.

    abstract：:RNA interference (RNAi) is a robust tool to study gene functions as well as potential for insect pest control. Finding suitable target genes is the key step in the development of an efficient RNAi-mediated pest control technique. Based on the transcriptome of Chilo suppressalis, 24 unigenes which putatively associated...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep28697

    authors： Zhu J,Dong YC,Li P,Niu CY

    更新日期：2016-06-29 00:00:00

  • Optically controlled spin-polarization memory effect on Mn delta-doped heterostructures.

    abstract：:We investigated the dynamics of the interaction between spin-polarized photo-created carriers and Mn ions on InGaAs/GaAs: Mn structures. The carriers are confined in an InGaAs quantum well and the Mn ions come from a Mn delta-layer grown at the GaAs barrier close to the well. Even though the carriers and the Mn ions a...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep24537

    authors： Balanta MA,Brasil MJ,Iikawa F,Mendes UC,Brum JA,Danilov YA,Dorokhin MV,Vikhrova OV,Zvonkov BN

    更新日期：2016-04-15 00:00:00

  • Speeding up bioproduction of selenium nanoparticles by using Vibrio natriegens as microbial factory.

    abstract：:Selenium and selenium nanoparticles (SeNPs) are extensively used in biomedicine, electronics and some other industrial applications. The bioproduction of SeNPs is gaining interest as a green method to manufacture these biotechnologically relevant products. Several microorganisms have been used for the production of Se...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-16252-1

    authors： Fernández-Llamosas H,Castro L,Blázquez ML,Díaz E,Carmona M

    更新日期：2017-11-22 00:00:00

  • Imaging mass spectrometry and MS/MS molecular networking reveals chemical interactions among cuticular bacteria and pathogenic fungi associated with fungus-growing ants.

    abstract：:The fungus-growing ant-microbe symbiosis is an ideal system to study chemistry-based microbial interactions due to the wealth of microbial interactions described, and the lack of information on the molecules involved therein. In this study, we employed a combination of MALDI imaging mass spectrometry (MALDI-IMS) and M...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-05515-6

    authors： Boya P CA,Fernández-Marín H,Mejía LC,Spadafora C,Dorrestein PC,Gutiérrez M

    更新日期：2017-07-17 00:00:00

  • AGE-RAGE signal generates a specific NF-κB RelA "barcode" that directs collagen I expression.

    abstract：:Advanced glycation end products (AGEs) are sugar-modified biomolecules that accumulate in the body with advancing age, and are implicated in the development of multiple age-associated structural and functional abnormities and diseases. It has been well documented that AGEs signal via their receptor RAGE to activate se...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep18822

    authors： Peng Y,Kim JM,Park HS,Yang A,Islam C,Lakatta EG,Lin L

    更新日期：2016-01-05 00:00:00

  • Role of the membrane potential in mitochondrial protein unfolding and import.

    abstract：:Newly synthesized mitochondrial precursor proteins have to become unfolded to cross the mitochondrial membranes. This unfolding is achieved primarily by mitochondrial Hsp70 (mtHsp70) for presequence-containing precursor proteins. However, the membrane potential across the inner membrane (ΔΨ) could also contribute to u...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-44152-z

    authors： Sato TK,Kawano S,Endo T

    更新日期：2019-05-21 00:00:00

  • Inverse Resolution Limit of Partition Density and Detecting Overlapping Communities by Link-Surprise.

    abstract：:Finding overlapping communities of complex networks remains a challenge in network science. To address this challenge, one of the widely used approaches is finding the communities of links by optimizing the objective function, partition density. In this study, we show that partition density suffers from inverse resolu...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-12432-1

    authors： Lee J,Zhang ZY,Lee J,Brooks BR,Ahn YY

    更新日期：2017-09-29 00:00:00

  • Fluorescence Polarization Switching from a Single Silicon Vacancy Colour Centre in Diamond.

    abstract：:Single-photon emitters with stable and uniform photoluminescence properties are important for quantum technology. However, in many cases, colour centres in diamond exhibit spectral diffusion and photoluminescence intensity fluctuation. It is therefore essential to investigate the dynamics of colour centres at the sing...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep12244

    authors： Liu Y,Chen G,Rong Y,McGuinness LP,Jelezko F,Tamura S,Tanii T,Teraji T,Onoda S,Ohshima T,Isoya J,Shinada T,Wu E,Zeng H

    更新日期：2015-07-23 00:00:00

  • Scattering of spoof surface plasmon polaritons in defect-rich THz waveguides.

    abstract：:We report on the first observation of 'Spoof' Surface Plasmon Polariton (SPP) scattering from surface defects on metal-coated 3D printed, corrugated THz waveguiding surfaces. Surface defects, a result of the printing process, are shown to assist the direct coupling of the incident free-space radiation into a spoof SPP...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-42412-6

    authors： Klein AK,Basden A,Hammler J,Tyas L,Cooke M,Balocco C,Zeze D,Girkin JM,Gallant A

    更新日期：2019-04-18 00:00:00

  • The Quasi-Coarse-Grained Dynamics Method to Unravel the Mesoscale Evolution of Defects/Damage during Shock Loading and Spall Failure of Polycrystalline Al Microstructures.

    abstract：:A long-standing problem in modeling of shock response of metals is the ability to model defect nucleation and evolution mechanisms during plastic deformation and failure at the mesoscales. This paper demonstrates the capability of the "quasi-coarse-grained dynamics" (QCGD) simulation method to unravel microstructural ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-12340-4

    authors： Agarwal G,Valisetty RR,Namburu RR,Rajendran AM,Dongare AM

    更新日期：2017-09-28 00:00:00

  • Yeast expression of mammalian Onzin and fungal FCR1 suggests ancestral functions of PLAC8 proteins in mitochondrial metabolism and DNA repair.

    abstract：:The cysteine-rich PLAC8 domain of unknown function occurs in proteins found in most Eukaryotes. PLAC8-proteins play important yet diverse roles in different organisms, such as control of cell proliferation in animals and plants or heavy metal resistance in plants and fungi. Mammalian Onzin can be either pro-proliferat...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-43136-3

    authors： Daghino S,Di Vietro L,Petiti L,Martino E,Dallabona C,Lodi T,Perotto S

    更新日期：2019-04-29 00:00:00

  • A Pilot Randomised Double-Blind Study of the Tolerability and efficacy of repetitive Transcranial Magnetic Stimulation on Persistent Post-Concussion Syndrome.

    abstract：:This study investigates the effect of Repetitive Transcranial Magnetic Stimulation (rTMS) on persistent post-concussion syndrome (PCS). The study design was a randomized (coin toss), placebo controlled, and double-blind study. Thirty-seven participants with PCS were assessed for eligibility; 22 were randomised and 18 ...

    journal_title：Scientific reports

    pub_type： 杂志文章,随机对照试验

    doi：10.1038/s41598-019-41923-6

    authors： Moussavi Z,Suleiman A,Rutherford G,Ranjbar Pouya O,Dastgheib Z,Zhang W,Salter J,Wang X,Mansouri B,Lithgow B

    更新日期：2019-04-02 00:00:00

  • A new structure of two-dimensional allotropes of group V elements.

    abstract：:The elemental two-dimensional (2D) materials such as graphene, silicene, germanene, and black phosphorus have attracted considerable attention due to their fascinating physical properties. Structurally they possess the honeycomb or distorted honeycomb lattices, which are composed of six-atom rings. Here we find a new ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep25423

    authors： Li P,Luo W

    更新日期：2016-05-06 00:00:00

  • Control of the interaction strength of photonic molecules by nanometer precise 3D fabrication.

    abstract：:Applications for high resolution 3D profiles, so-called grayscale lithography, exist in diverse fields such as optics, nanofluidics and tribology. All of them require the fabrication of patterns with reliable absolute patterning depth independent of the substrate location and target materials. Here we present a comple...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-16496-x

    authors： Rawlings CD,Zientek M,Spieser M,Urbonas D,Stöferle T,Mahrt RF,Lisunova Y,Brugger J,Duerig U,Knoll AW

    更新日期：2017-11-28 00:00:00

  • Alpha-lipoic acid ameliorates the epithelial mesenchymal transition induced by unilateral ureteral obstruction in mice.

    abstract：:The epithelial-to-mesenchymal transition (EMT) is one of mechanisms that induce renal interstitial fibrosis. Understanding EMT in renal fibrosis has important therapeutic implications for patients with kidney disease. Alpha-lipoic acid (ALA) is a natural compound with antioxidant properties. Studies for ALA are perfor...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep46065

    authors： Cho HS,Kim JH,Jang HN,Lee TW,Jung MH,Kim TH,Chang SH,Park DJ

    更新日期：2017-04-05 00:00:00

  • Microfluidic Sorting of Cells by Viability Based on Differences in Cell Stiffness.

    abstract：:The enrichment of viable cells is an essential step to obtain effective products for cell therapy. While procedures exist to characterize the viability of cells, most methods to exclude nonviable cells require the use of density gradient centrifugation or antibody-based cell sorting with molecular labels of cell viabi...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-01807-z

    authors： Islam M,Brink H,Blanche S,DiPrete C,Bongiorno T,Stone N,Liu A,Philip A,Wang G,Lam W,Alexeev A,Waller EK,Sulchek T

    更新日期：2017-05-17 00:00:00

  • Oxytocin attenuates feelings of hostility depending on emotional context and individuals' characteristics.

    abstract：:In humans, oxytocin (OT) enhances prosocial behaviour. However, it is still unclear how the prosocial effects of OT are modulated by emotional features and/or individuals' characteristics. In a placebo-controlled design, we tested 20 healthy male volunteers to investigate these behavioural and neurophysiological modul...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep00384

    authors： Hirosawa T,Kikuchi M,Higashida H,Okumura E,Ueno S,Shitamichi K,Yoshimura Y,Munesue T,Tsubokawa T,Haruta Y,Nakatani H,Hashimoto T,Minabe Y

    更新日期：2012-01-01 00:00:00

  • Electrospun Fibrous Membranes with Super-large-strain Electric Superhydrophobicity.

    abstract：:Large-strain elastic superhydrophobicity is highly desirable for its enhanced use performance and functional reliability in mechanically dynamic environments, but remains challenging to develop. Here we have, for the first time, proven that an elastic fibrous membrane after surface hydrophobization can maintain superh...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep15863

    authors： Zhou H,Wang H,Niu H,Lin T

    更新日期：2015-10-29 00:00:00

  • Nanosecond light induced, thermally tunable transient dual absorption bands in a-Ge₅As₃₀Se₆₅ thin film.

    abstract：:In this article, we report the first observation of nanosecond laser induced transient dual absorption bands, one in the bandgap (TA₁) and another in the sub-bandgap (TA₂) regions of a-Ge₅As₃₀Se₆₅ thin films. Strikingly, these bands are thermally tunable and exhibit a unique contrasting characteristic: the magnitude o...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep06573

    authors： Khan P,Saxena T,Jain H,Adarsh KV

    更新日期：2014-10-10 00:00:00

  • Phycosynthesis and Enhanced Photocatalytic Activity of Zinc Oxide Nanoparticles Toward Organosulfur Pollutants.

    abstract：:A novel eco-friendly procedure was developed to produce safer, stable and highly pure zinc oxide nanoparticles (ZnO NPs) using microalgae Chlorella extract. The ZnO NPs were synthesized simply using zinc nitrate and microalgae Chlorella extract which conducted at ambient conditions. In this recipe, microalgae Chlorell...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-43368-3

    authors： Khalafi T,Buazar F,Ghanemi K

    更新日期：2019-05-03 00:00:00

  • Water channel pore size determines exclusion properties but not solute selectivity.

    abstract：:Aquaporins (AQPs) are a ubiquitous family of transmembrane water channel proteins. A subgroup of AQP water channels also facilitates transmembrane diffusion of small, polar solutes. A constriction within the pore, the aromatic/arginine (ar/R) selectivity filter, is thought to control solute permeability: previous stud...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-56814-z

    authors： Kitchen P,Salman MM,Pickel SU,Jennings J,Törnroth-Horsefield S,Conner MT,Bill RM,Conner AC

    更新日期：2019-12-30 00:00:00

  • Identification of Small Molecule Enhancers of Immunotherapy for Melanoma.

    abstract：:Small molecule based targeted therapies for the treatment of metastatic melanoma hold promise but responses are often not durable, and tumors frequently relapse. Response to adoptive cell transfer (ACT)-based immunotherapy in melanoma patients are durable but patients develop resistance primarily due to loss of antige...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-62369-1

    authors： Dextras C,Dashnyam M,Griner LAM,Sundaresan J,Chim B,Yu Z,Vodnala S,Lee CR,Hu X,Southall N,Marugan JJ,Jadhav A,Restifo NP,Acquavella N,Ferrer M,Singh A

    更新日期：2020-03-30 00:00:00

  • Moonlighting transcriptional activation function of a fungal sulfur metabolism enzyme.

    abstract：:Moonlighting proteins, including metabolic enzymes acting as transcription factors (TF), are present in a variety of organisms but have not been described in higher fungi so far. In a previous genome-wide analysis of the TF repertoire of the plant-symbiotic fungus Tuber melanosporum, we identified various enzymes, inc...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep25165

    authors： Levati E,Sartini S,Bolchi A,Ottonello S,Montanini B

    更新日期：2016-04-28 00:00:00

  • Classification of Tandem Mass Spectra for Identification of N- and O-linked Glycopeptides.

    abstract：:Analysis of intact glycopeptides by mass spectrometry is essential to determining the microheterogeneity of protein glycosylation. Higher-energy collisional dissociation (HCD) fragmentation of glycopeptides generates mono- or disaccharide ions called oxonium ions that carry information about the structure of the fragm...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep37189

    authors： Toghi Eshghi S,Yang W,Hu Y,Shah P,Sun S,Li X,Zhang H

    更新日期：2016-11-21 00:00:00

  • Global prevalence and distribution of vancomycin resistant, vancomycin intermediate and heterogeneously vancomycin intermediate Staphylococcus aureus clinical isolates: a systematic review and meta-analysis.

    abstract：:Vancomycin-resistant Staphylococcus aureus (VRSA), Vancomycin-intermediate S. aureus (VISA) and heterogeneous VISA (hVISA) are subject to vancomycin treatment failure. The aim of the present study was to determine their precise prevalence and investigate prevalence variability depending on different years and location...

    journal_title：Scientific reports

    pub_type： 杂志文章,meta分析

    doi：10.1038/s41598-020-69058-z

    authors： Shariati A,Dadashi M,Moghadam MT,van Belkum A,Yaslianifard S,Darban-Sarokhalil D

    更新日期：2020-07-29 00:00:00

  • Internal Motion Estimation by Internal-external Motion Modeling for Lung Cancer Radiotherapy.

    abstract：:The aim of this study is to develop an internal-external correlation model for internal motion estimation for lung cancer radiotherapy. Deformation vector fields that characterize the internal-external motion are obtained by respectively registering the internal organ meshes and external surface meshes from the 4DCT i...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-22023-3

    authors： Chen H,Zhong Z,Yang Y,Chen J,Zhou L,Zhen X,Gu X

    更新日期：2018-02-27 00:00:00

  • Chronic exposure to low doses of estradiol-17ß increases blood pressure in young female rats: A possible role for central Endothelin-1.

    abstract：:Previously, we demonstrated that chronic exposure to low levels of estradiol-17β (E2) increases mean arterial pressure (MAP) in young female Sprague-Dawley (SD) rats, however, the underlying mechanisms are unclear. Since endothelin-1 (ET-1) is implicated in blood pressure (BP) regulation, we hypothesized that E2's eff...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-00213-9

    authors： Subramanian M,MohanKumar SM,Balasubramanian P,Northcott CA,Garver H,Fink GD,MohanKumar PS

    更新日期：2017-03-10 00:00:00

  • Comparisons of conventional and novel anthropometric obesity indices to predict metabolic syndrome among vegetarians in Malaysia.

    abstract：:Our study aimed to compare the ability of anthropometric obesity indices to predict MetS and to determine the sex-specific optimal cut-off values for MetS among Malaysian vegetarians. Body weight, height, waist circumference (WC), blood pressure (BP), fasting venous blood sample were collected from 273 vegetarians in ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-78035-5

    authors： Ching YK,Chin YS,Appukutty M,Gan WY,Chan YM

    更新日期：2020-11-30 00:00:00