1
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Adampourezare M, Hasanzadeh M, Seidi F. Microfluidic assisted recognition of miRNAs towards point-of-care diagnosis: Technical and analytical overview towards biosensing of short stranded single non-coding oligonucleotides. Biomed Pharmacother 2022; 153:113365. [PMID: 35785705 DOI: 10.1016/j.biopha.2022.113365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/02/2022] Open
Abstract
MiRNAs are short stranded single non-coding oligonucleotides that play an important role in regulating gene expression. MiRNAs are stable in RNase enriched environments such as human body fluids and their dysregulation or abnormal abundance in human body fluids as a diagnostic biomarker has been associated with several diseases. Due to the low concentration of miRNAs, it is difficult to detect using interactive methods (ideal detection limit is femtomolar range). However, clinicians lack sensitive and reliable methods for quantifying miRNA. Microfluidic devices integrated with electrochemical, optical (fluorometric, SERs, FRET, colorimetric), electrochemiluminescence and photoelectrochemical signal readout led to development innovative diagnostic device test, can probably overcome the limitations of the traditional methods. In the present review, microfluid methods for the sensitive and selective recognition of miRNA in various biological matrices are surveyed. Also, advantages and limitation of recognition methods on the performance and efficiency of microfluidic based biosensing of miRNAs are critically investigated. Finally, the future perspectives on the diagnosis of disease based on microfluidic analysis of miRNAs are provided.
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Affiliation(s)
- Mina Adampourezare
- Department of Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran; Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Nutrition Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Farzad Seidi
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
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2
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Oguchi Y, Ozaki Y, Abdelmoez MN, Shintaku H. NanoSINC-seq dissects the isoform diversity in subcellular compartments of single cells. SCIENCE ADVANCES 2021; 7:7/15/eabe0317. [PMID: 33827812 PMCID: PMC8026137 DOI: 10.1126/sciadv.abe0317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
Alternative mRNA isoforms play a key role in generating diverse protein isoforms. To dissect isoform usage in the subcellular compartments of single cells, we introduced an novel approach, nanopore sequencing coupled with single-cell integrated nuclear and cytoplasmic RNA sequencing, that couples microfluidic fractionation, which separates cytoplasmic RNA from nuclear RNA, with full-length complementary DNA (cDNA) sequencing using a nanopore sequencer. Leveraging full-length cDNA reads, we found that the nuclear transcripts are notably more diverse than cytoplasmic transcripts. Our findings also indicated that transcriptional noise emanating from the nucleus is regulated across the nuclear membrane and then either attenuated or amplified in the cytoplasm depending on the function involved. Overall, our results provide the landscape that shows how the transcriptional noise arising from the nucleus propagates to the cytoplasm.
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Affiliation(s)
- Yusuke Oguchi
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Yuka Ozaki
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, Japan
| | | | - Hirofumi Shintaku
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, Japan.
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3
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Lee H, Lee J, Lee SG, Doyle PS. Hydrogel-Based Colorimetric Assay for Multiplexed MicroRNA Detection in a Microfluidic Device. Anal Chem 2020; 92:5750-5755. [PMID: 32207967 PMCID: PMC7178251 DOI: 10.1021/acs.analchem.9b05043] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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Although microRNA
(miRNA) expression levels provide important information
regarding disease states owing to their unique dysregulation patterns
in tissues, translation of miRNA diagnostics into point-of-care (POC)
settings has been limited by practical challenges. Here, we developed
a hydrogel-based microfluidic platform for colorimetric profiling
of miRNAs, without the use of complex external equipment for fluidics
and imaging. For sensitive and reliable measurement without the risk
of sequence bias, we employed a gold deposition-based signal amplification
scheme and dark-field imaging, and seamlessly integrated a previously
developed miRNA assay scheme into this platform. The assay demonstrated
a limit of detection of 260 fM, along with multiplexing of small panels
of miRNAs in healthy and cancer samples. We anticipate this versatile
platform to facilitate a broad range of POC profiling of miRNAs in
cancer-associated dysregulation with high-confidence by exploiting
the unique features of hydrogel substrate in an on-chip format and
colorimetric analysis.
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Affiliation(s)
- Hyewon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Jiseok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, The United States
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4
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Kim J, Sahloul S, Orozaliev A, Do VQ, Pham VS, Martins D, Wei X, Levicky R, Song YA. Microfluidic Electrokinetic Preconcentration Chips: Enhancing the detection of nucleic acids and exosomes. IEEE NANOTECHNOLOGY MAGAZINE 2020. [DOI: 10.1109/mnano.2020.2966064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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5
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Dziomba S, Ciura K, Dawid M. The on-line preconcentration of nanoparticles in electromigration techniques. J Chromatogr A 2019; 1606:360332. [PMID: 31262513 DOI: 10.1016/j.chroma.2019.06.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023]
Abstract
Electromigration techniques have recently emerged as an alternative analytical tool for nanoparticles characterization. Due to the high throughput capability and separation efficiency their application for detection/quantification of nanomaterials in samples of various origin has attracted much attention. While the electromigration techniques are known to suffer from insufficient detection sensitivity, a number of papers investigating on-line preconcentration of nanoparticles in capillary electrophoresis was addressed to the issue. In this work the available literature on nanoparticles stacking in electrodriven separation techniques was reviewed. The discussion was supported by theoretical background. A special emphasis was put on the stability of nanoparticles dispersion during electrophoretic process. The considerations on future perspectives were included in final remarks.
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Affiliation(s)
- Szymon Dziomba
- Department of Toxicology, Faculty of Pharmacy, Medical University of Gdansk, 107 Hallera Street, 80-416 Gdansk, Poland.
| | - Krzesimir Ciura
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdansk, 107 Hallera Street, 80-416 Gdansk, Poland
| | - Marta Dawid
- Department of Toxicology, Faculty of Pharmacy, Medical University of Gdansk, 107 Hallera Street, 80-416 Gdansk, Poland
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6
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Abstract
This review discusses research developments and applications of isotachophoresis (ITP) to the initiation, control, and acceleration of chemical reactions, emphasizing reactions involving biomolecular reactants such as nucleic acids, proteins, and live cells. ITP is a versatile technique which requires no specific geometric design or material, and is compatible with a wide range of microfluidic and automated platforms. Though ITP has traditionally been used as a purification and separation technique, recent years have seen its emergence as a method to automate and speed up chemical reactions. ITP has been used to demonstrate up to 14 000-fold acceleration of nucleic acid assays, and has been used to enhance lateral flow and other immunoassays, and even whole bacterial cell detection assays. We here classify these studies into two categories: homogeneous (all reactants in solution) and heterogeneous (at least one reactant immobilized on a solid surface) assay configurations. For each category, we review and describe physical modeling and scaling of ITP-aided reaction assays, and elucidate key principles in ITP assay design. We summarize experimental advances, and identify common threads and approaches which researchers have used to optimize assay performance. Lastly, we propose unaddressed challenges and opportunities that could further improve these applications of ITP.
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Affiliation(s)
- C Eid
- Department of Mechanical Engineering, Stanford University, USA.
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7
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Mayer M, Takegami S, Neumeier M, Rink S, Jacobi von Wangelin A, Schulte S, Vollmer M, Griesbeck AG, Duerkop A, Baeumner AJ. Electrochemiluminescence Bioassays with a Water-Soluble Luminol Derivative Can Outperform Fluorescence Assays. Angew Chem Int Ed Engl 2017; 57:408-411. [DOI: 10.1002/anie.201708630] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/18/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Michael Mayer
- Institute of Analytical Chemistry/ Chemo-and Biosensors; University of Regensburg; Universitätsstraße 31 93053 Regensburg Germany
| | - Shigehiko Takegami
- Department of Analytical Chemistry; Kyoto Pharmaceutical; University Japan
| | - Michael Neumeier
- Institute of Organic Chemistry; University of; Regensburg Germany
| | - Simone Rink
- Institute of Analytical Chemistry/ Chemo-and Biosensors; University of Regensburg; Universitätsstraße 31 93053 Regensburg Germany
| | | | - Silja Schulte
- Institute of Organic Chemistry; University of; Cologne Germany
| | - Moritz Vollmer
- Institute of Organic Chemistry; University of; Cologne Germany
| | | | - Axel Duerkop
- Institute of Analytical Chemistry/ Chemo-and Biosensors; University of Regensburg; Universitätsstraße 31 93053 Regensburg Germany
| | - Antje J. Baeumner
- Institute of Analytical Chemistry/ Chemo-and Biosensors; University of Regensburg; Universitätsstraße 31 93053 Regensburg Germany
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8
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Mayer M, Takegami S, Neumeier M, Rink S, Jacobi von Wangelin A, Schulte S, Vollmer M, Griesbeck AG, Duerkop A, Baeumner AJ. Elektrochemilumineszenz-Bioassays können Fluoreszenzassays mithilfe eines wasserlöslichen Luminolderivats übertreffen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708630] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michael Mayer
- Institut für Analytische Chemie, Chemo- und Biosensorik; Universität Regensburg; Universitätsstraße 31 93053 Regensburg Deutschland
| | - Shigehiko Takegami
- Department of Analytical Chemistry; Kyoto Pharmaceutical University; Japan
| | - Michael Neumeier
- Institut für Organische Chemie; Universität Regensburg; Deutschland
| | - Simone Rink
- Institut für Analytische Chemie, Chemo- und Biosensorik; Universität Regensburg; Universitätsstraße 31 93053 Regensburg Deutschland
| | | | - Silja Schulte
- Department für Chemie, Organische Chemie; Universität zu Köln; Deutschland
| | - Moritz Vollmer
- Department für Chemie, Organische Chemie; Universität zu Köln; Deutschland
| | - Axel G. Griesbeck
- Department für Chemie, Organische Chemie; Universität zu Köln; Deutschland
| | - Axel Duerkop
- Institut für Analytische Chemie, Chemo- und Biosensorik; Universität Regensburg; Universitätsstraße 31 93053 Regensburg Deutschland
| | - Antje J. Baeumner
- Institut für Analytische Chemie, Chemo- und Biosensorik; Universität Regensburg; Universitätsstraße 31 93053 Regensburg Deutschland
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9
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Datinská V, Voráčová I, Schlecht U, Berka J, Foret F. Recent progress in nucleic acids isotachophoresis. J Sep Sci 2017; 41:236-247. [DOI: 10.1002/jssc.201700878] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 01/30/2023]
Affiliation(s)
- Vladimíra Datinská
- Czech Academy of Sciences; Institute of Analytical Chemistry; Brno Czech Republic
- Masaryk University; Faculty of Science; Brno Czech Republic
| | - Ivona Voráčová
- Czech Academy of Sciences; Institute of Analytical Chemistry; Brno Czech Republic
| | | | - Jan Berka
- Roche Sequencing Solutions, Inc; Pleasanton CA USA
| | - František Foret
- Czech Academy of Sciences; Institute of Analytical Chemistry; Brno Czech Republic
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10
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Eid C, Branda SS, Meagher RJ. A rapidly-prototyped microfluidic device for size-based nucleic acid fractionation using isotachophoresis. Analyst 2017; 142:2094-2099. [DOI: 10.1039/c7an00431a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a novel microfluidic device for size-based nucleic acid (NA) fractionation using isotachophoresis (ITP) and an ionic spacer.
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Affiliation(s)
- C. Eid
- Department of Mechanical Engineering
- Stanford University
- USA
| | - S. S. Branda
- Biomass Science and Conversion Technology Department
- Sandia National Laboratories
- USA
| | - R. J. Meagher
- Biotechnology and Bioengineering Department
- Sandia National Laboratories
- USA
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11
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Malá Z, Gebauer P, Boček P. Analytical capillary isotachophoresis after 50 years of development: Recent progress 2014-2016. Electrophoresis 2016; 38:9-19. [DOI: 10.1002/elps.201600289] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Zdena Malá
- Institute of Analytical Chemistry of the Czech Academy of Sciences; v.v.i; Brno Czech Republic
| | - Petr Gebauer
- Institute of Analytical Chemistry of the Czech Academy of Sciences; v.v.i; Brno Czech Republic
| | - Petr Boček
- Institute of Analytical Chemistry of the Czech Academy of Sciences; v.v.i; Brno Czech Republic
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12
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Exploring Gradients in Electrophoretic Separation and Preconcentration on Miniaturized Devices. SEPARATIONS 2016. [DOI: 10.3390/separations3020012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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13
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Martins D, Wei X, Levicky R, Song YA. Integration of Multiplexed Microfluidic Electrokinetic Concentrators with a Morpholino Microarray via Reversible Surface Bonding for Enhanced DNA Hybridization. Anal Chem 2016; 88:3539-47. [PMID: 26916577 DOI: 10.1021/acs.analchem.5b03875] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
UNLABELLED We describe a microfluidic concentration device to accelerate the surface hybridization reaction between DNA and morpholinos (MOs) for enhanced detection. The microfluidic concentrator comprises a single polydimethylsiloxane (PDMS) microchannel onto which an ion-selective layer of conductive polymer poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) ( PEDOT PSS) was directly printed and then reversibly surface bonded onto a morpholino microarray for hybridization. Using this electrokinetic trapping concentrator, we could achieve a maximum concentration factor of ∼800 for DNA and a limit of detection of 10 nM within 15 min. In terms of the detection speed, it enabled faster hybridization by around 10-fold when compared to conventional diffusion-based hybridization. A significant advantage of our approach is that the fabrication of the microfluidic concentrator is completely decoupled from the microarray; by eliminating the need to deposit an ion-selective layer on the microarray surface prior to device integration, interfacing between both modules, the PDMS chip for electrokinetic concentration and the substrate for DNA sensing are easier and applicable to any microarray platform. Furthermore, this fabrication strategy facilitates a multiplexing of concentrators. We have demonstrated the proof-of-concept for multiplexing by building a device with 5 parallel concentrators connected to a single inlet/outlet and applying it to parallel concentration and hybridization. Such device yielded similar concentration and hybridization efficiency compared to that of a single-channel device without adding any complexity to the fabrication and setup. These results demonstrate that our concentrator concept can be applied to the development of a highly multiplexed concentrator-enhanced microarray detection system for either genetic analysis or other diagnostic assays.
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Affiliation(s)
- Diogo Martins
- Division of Engineering, New York University Abu Dhabi , P.O. Box 129188 , Abu Dhabi, United Arab Emirates
| | - Xi Wei
- Division of Engineering, New York University Abu Dhabi , P.O. Box 129188 , Abu Dhabi, United Arab Emirates.,Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering , Brooklyn, New York 11201, United States
| | - Rastislav Levicky
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering , Brooklyn, New York 11201, United States
| | - Yong-Ak Song
- Division of Engineering, New York University Abu Dhabi , P.O. Box 129188 , Abu Dhabi, United Arab Emirates.,Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering , Brooklyn, New York 11201, United States
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14
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Kuriyama K, Shintaku H, Santiago JG. Isotachophoresis for fractionation and recovery of cytoplasmic RNA and nucleus from single cells. Electrophoresis 2015; 36:1658-62. [PMID: 25820552 DOI: 10.1002/elps.201500040] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/13/2015] [Accepted: 03/14/2015] [Indexed: 12/26/2022]
Abstract
There is a substantial need for simultaneous analyses of RNA and DNA from individual single cells. Such analysis provides unique evidence of cell-to-cell differences and the correlation between gene expression and genomic mutation in highly heterogeneous cell populations. We present a novel microfluidic system that leverages isotachophoresis to fractionate and isolate cytoplasmic RNA and genomic DNA (gDNA) from single cells. The system uniquely enables independent, sequence-specific analyses of these critical markers. Our system uses a microfluidic chip with a simple geometry and four end-channel electrodes, and completes the entire process in <5 min, including lysis, purification, fractionation, and delivery to DNA and RNA output reservoirs, each containing high quality and purity aliquots with no measurable cross-contamination of cytoplasmic RNA versus gDNA. We demonstrate our system with simultaneous, sequence-specific quantitation using off-chip RT-qPCR and qPCR for simultaneous cytoplasmic RNA and gDNA analyses, respectively.
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Affiliation(s)
- Kentaro Kuriyama
- Department of Mechanical Engineering, Stanford University, Escondido, Stanford, CA, USA
| | - Hirofumi Shintaku
- Department of Mechanical Engineering, Stanford University, Escondido, Stanford, CA, USA.,Department of Micro Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Escondido, Stanford, CA, USA
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