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Abstract
Isotachophoresis (ITP) is a versatile electrophoretic technique that can be used for sample preconcentration, separation, purification, and mixing, and to control and accelerate chemical reactions. Although the basic technique is nearly a century old and widely used, there is a persistent need for an easily approachable, succinct, and rigorous review of ITP theory and analysis. This is important because the interest and adoption of the technique has grown over the last two decades, especially with its implementation in microfluidics and integration with on-chip chemical and biochemical assays. We here provide a review of ITP theory starting from physicochemical first-principles, including conservation of species, conservation of current, approximation of charge neutrality, pH equilibrium of weak electrolytes, and so-called regulating functions that govern transport dynamics, with a strong emphasis on steady and unsteady transport. We combine these generally applicable (to all types of ITP) theoretical discussions with applications of ITP in the field of microfluidic systems, particularly on-chip biochemical analyses. Our discussion includes principles that govern the ITP focusing of weak and strong electrolytes; ITP dynamics in peak and plateau modes; a review of simulation tools, experimental tools, and detection methods; applications of ITP for on-chip separations and trace analyte manipulation; and design considerations and challenges for microfluidic ITP systems. We conclude with remarks on possible future research directions. The intent of this review is to help make ITP analysis and design principles more accessible to the scientific and engineering communities and to provide a rigorous basis for the increased adoption of ITP in microfluidics.
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Affiliation(s)
- Ashwin Ramachandran
- Department of Aeronautics and Astronautics, Stanford University, Stanford, California 94305, United States
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
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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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Subramanian Parimalam S, Abdelmoez MN, Tsuchida A, Sotta N, Tanaka M, Kuromori T, Fujiwara T, Hirai MY, Yokokawa R, Oguchi Y, Shintaku H. Targeted permeabilization of the cell wall and extraction of charged molecules from single cells in intact plant clusters using a focused electric field. Analyst 2021; 146:1604-1611. [PMID: 33624642 DOI: 10.1039/d0an02163f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The extraction of cellular contents from plant cells covered with cell walls remains a challenge, as it is physically hindered by the cell wall. We present a new microfluidic approach that leverages an intense pulsed electric field for permeabilizing the cell wall and a focused DC electric field for extracting the cellular contents selectively from a few targeted cells in a cluster of intact plant cells. We coupled the approach with on-chip fluorescence quantification of extracted molecules leveraging isotachophoresis as well as off-chip reverse transcription-quantitative polymerase chain reaction detecting extracted mRNA molecules. Our approach offers a workflow of about 5 min, isolating a cluster of intact plant cells, permeabilizing the cell wall, selectively extracting cytosolic molecules from a few targeted cells in the cluster, and outputting them to off-chip analyses without any enzymatic reactions. We anticipate that this approach will create a new opportunity to explore plant biology through less biased data realized by the rapid extraction of molecules from intact plant clusters.
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4
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Khnouf R, Shore S, Han CM, Henderson JM, Munro SA, McCaffrey AP, Shintaku H, Santiago JG. Efficient Production of On-Target Reads for Small RNA Sequencing of Single Cells Using Modified Adapters. Anal Chem 2018; 90:12609-12615. [PMID: 30260208 PMCID: PMC6233959 DOI: 10.1021/acs.analchem.8b02773] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Although
single-cell mRNA sequencing has been a powerful tool to explore cellular
heterogeneity, the sequencing of small RNA at the single-cell level
(sc-sRNA-seq) remains a challenge, as these have no consensus sequence,
are relatively low abundant, and are difficult to amplify in a bias-free
fashion. We present two methods of single-cell-lysis that enable sc-sRNA-seq.
The first method is a chemical-based technique with overnight freezing
while the second method leverages on-chip electrical lysis of plasma
membrane and physical extraction and separation of cytoplasmic RNA
via isotachophoresis. We coupled these two methods with off-chip small
RNA library preparation using CleanTag modified adapters to prevent
the formation of adapter dimers. We then demonstrated sc-sRNA-seq
with single K562 human leukemic cells. Our approaches offer a relatively
short hands-on time of 6 h and efficient generation of on-target reads.
The sc-sRNA-seq with our approaches showed detection of miRNA with
various abundances ranging from 16 000 copies/cell to about
10 copies/cell. We anticipate this approach will create a new opportunity
to explore cellular heterogeneity through small RNA expression.
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Affiliation(s)
- Ruba Khnouf
- Department of Mechanical Engineering , Stanford University , Stanford , California 94305 , United States.,Department of Biomedical Engineering , Jordan University of Science and Technology , Irbid 22110 , Jordan
| | - Sabrina Shore
- TriLink Biotechnologies LLC , San Diego , California 92121 , United States
| | - Crystal M Han
- Joint Initiative for Metrology in Biology , National Institute of Standards and Technology , Stanford , California 94305 , United States.,Department of Mechanical Engineering , San Jose State University , San Jose , California 95192 , United States
| | | | - Sarah A Munro
- Joint Initiative for Metrology in Biology , National Institute of Standards and Technology , Stanford , California 94305 , United States.,Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Anton P McCaffrey
- TriLink Biotechnologies LLC , San Diego , California 92121 , United States
| | - Hirofumi Shintaku
- RIKEN Cluster for Pioneering Research , Wako , Saitama 351-0198 , Japan
| | - Juan G Santiago
- Department of Mechanical Engineering , Stanford University , Stanford , California 94305 , United States
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5
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Abdelmoez MN, Iida K, Oguchi Y, Nishikii H, Yokokawa R, Kotera H, Uemura S, Santiago JG, Shintaku H. SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology. Genome Biol 2018; 19:66. [PMID: 29871653 PMCID: PMC5989370 DOI: 10.1186/s13059-018-1446-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 05/07/2018] [Indexed: 02/07/2023] Open
Abstract
We report a microfluidic system that physically separates nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) from a single cell and enables single-cell integrated nucRNA and cytRNA-sequencing (SINC-seq). SINC-seq constructs two individual RNA-seq libraries, nucRNA and cytRNA, per cell, quantifies gene expression in the subcellular compartments, and combines them to create novel single-cell RNA-seq data. Leveraging SINC-seq, we discover distinct natures of correlation among cytRNA and nucRNA that reflect the transient physiological state of single cells. These data provide unique insights into the regulatory network of messenger RNA from the nucleus toward the cytoplasm at the single-cell level.
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Affiliation(s)
- Mahmoud N Abdelmoez
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan.,Microfluidics RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Kei Iida
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Oguchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hidekazu Nishikii
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Ryuji Yokokawa
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Hidetoshi Kotera
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA
| | - Hirofumi Shintaku
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan. .,Microfluidics RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research, Saitama, Japan.
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