1
|
Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greenleaf WJ, Gordân R, Zeitlinger J, Kundaje A, Fordyce PM. Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science 2023; 381:eadd1250. [PMID: 37733848 DOI: 10.1126/science.add1250] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/26/2023] [Indexed: 09/23/2023]
Abstract
Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter gene expression, yet how they regulate transcription remains unknown. We found that STRs modulate transcription factor (TF)-DNA affinities and apparent on-rates by about 70-fold by directly binding TF DNA-binding domains, with energetic impacts exceeding many consensus motif mutations. STRs maximize the number of weakly preferred microstates near target sites, thereby increasing TF density, with impacts well predicted by statistical mechanics. Confirming that STRs also affect TF binding in cells, neural networks trained only on in vivo occupancies predicted effects identical to those observed in vitro. Approximately 90% of TFs preferentially bound STRs that need not resemble known motifs, providing a cis-regulatory mechanism to target TFs to genomic sites.
Collapse
Affiliation(s)
- Connor A Horton
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Amr M Alexandari
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Michael G B Hayes
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Emil Marklund
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julia M Schaepe
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Arjun K Aditham
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Nilay Shah
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Peter H Suzuki
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Avanti Shrikumar
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Ariel Afek
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Computer Science, Duke University, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- The University of Kansas Medical Center, Kansas City, KS 66103, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Polly M Fordyce
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94110, USA
| |
Collapse
|
2
|
Yang H, Tel J. Engineering global and local signal generators for probing temporal and spatial cellular signaling dynamics. Front Bioeng Biotechnol 2023; 11:1239026. [PMID: 37790255 PMCID: PMC10543096 DOI: 10.3389/fbioe.2023.1239026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/16/2023] [Indexed: 10/05/2023] Open
Abstract
Cells constantly encounter a wide range of environmental signals and rely on their signaling pathways to initiate reliable responses. Understanding the underlying signaling mechanisms and cellular behaviors requires signal generators capable of providing diverse input signals to deliver to cell systems. Current research efforts are primarily focused on exploring cellular responses to global or local signals, which enable us to understand cellular signaling and behavior in distinct dimensions. This review presents recent advancements in global and local signal generators, highlighting their applications in studying temporal and spatial signaling activity. Global signals can be generated using microfluidic or photochemical approaches. Local signal sources can be created using living or artificial cells in combination with different control methods. We also address the strengths and limitations of each signal generator type, discussing challenges and potential extensions for future research. These approaches are expected to continue to facilitate on-going research to discover novel and intriguing cellular signaling mechanisms.
Collapse
Affiliation(s)
- Haowen Yang
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| |
Collapse
|
3
|
Ahrar S, Raje M, Lee IC, Hui EE. Pneumatic computers for embedded control of microfluidics. SCIENCE ADVANCES 2023; 9:eadg0201. [PMID: 37267360 PMCID: PMC10413662 DOI: 10.1126/sciadv.adg0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 04/28/2023] [Indexed: 06/04/2023]
Abstract
Alternative computing approaches that interface readily with physical systems are well suited for embedded control of those systems. We demonstrate finite state machines implemented as pneumatic circuits of microfluidic valves and use these controllers to direct microfluidic liquid handling procedures on the same chip. These monolithic integrated systems require only power to be supplied externally, in the form of a vacuum source. User input can be provided directly to the chip by covering pneumatic ports with a finger. State machines with up to four bits of state memory are demonstrated, and next-state combinational logic can be fully reprogrammed by changing the hole-punch pattern on a membrane in the chip. These pneumatic computers demonstrate a framework for the embedded control of physical systems and open a path to stand-alone lab-on-a-chip devices capable of highly complex functionality.
Collapse
Affiliation(s)
- Siavash Ahrar
- Department of Biomedical Engineering, University of California, Irvine, CA, USA
- Department of Biomedical Engineering, California State University, Long Beach, CA, USA
| | - Manasi Raje
- Department of Biomedical Engineering, University of California, Irvine, CA, USA
| | - Irene C. Lee
- Department of Biomedical Engineering, University of California, Irvine, CA, USA
| | - Elliot E. Hui
- Department of Biomedical Engineering, University of California, Irvine, CA, USA
| |
Collapse
|
4
|
Nguyen M, Tong A, Volosov M, Madhavarapu S, Freeman J, Voronov R. Addressable microfluidics technology for non-sacrificial analysis of biomaterial implants in vivo. BIOMICROFLUIDICS 2023; 17:024103. [PMID: 37035100 PMCID: PMC10076065 DOI: 10.1063/5.0137932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/06/2023] [Indexed: 06/19/2023]
Abstract
Tissue regeneration-promoting and drug-eluting biomaterials are commonly implanted into animals as a part of late-stage testing before committing to human trials required by the government. Because the trials are very expensive (e.g., they can cost over a billion U.S. dollars), it is critical for companies to have the best possible characterization of the materials' safety and efficacy before it goes into a human. However, the conventional approaches to biomaterial evaluation necessitate sacrificial analysis (i.e., euthanizing a different animal for measuring each time point and retrieving the implant for histological analysis), due to the inability to monitor how the host tissues respond to the presence of the material in situ. This is expensive, inaccurate, discontinuous, and unethical. In contrast, our manuscript presents a novel microfluidic platform potentially capable of performing non-disruptive fluid manipulations within the spatial constraints of an 8 mm diameter critical calvarial defect-a "gold standard" model for testing engineered bone tissue scaffolds in living animals. In particular, here, addressable microfluidic plumbing is specifically adapted for the in vivo implantation into a simulated rat's skull, and is integrated with a combinatorial multiplexer for a better scaling of many time points and/or biological signal measurements. The collected samples (modeled as food dyes for proof of concept) are then transported, stored, and analyzed ex vivo, which adds previously-unavailable ease and flexibility. Furthermore, care is taken to maintain a fluid equilibrium in the simulated animal's head during the sampling to avoid damage to the host and to the implant. Ultimately, future implantation protocols and technology improvements are envisioned toward the end of the manuscript. Although the bone tissue engineering application was chosen as a proof of concept, with further work, the technology is potentially versatile enough for other in vivo sampling applications. Hence, the successful outcomes of its advancement should benefit companies developing, testing, and producing vaccines and drugs by accelerating the translation of advanced cell culturing tech to the clinical market. Moreover, the nondestructive monitoring of the in vivo environment can lower animal experiment costs and provide data-gathering continuity superior to the conventional destructive analysis. Lastly, the reduction of sacrifices stemming from the use of this technology would make future animal experiments more ethical.
Collapse
Affiliation(s)
- Minh Nguyen
- Otto H. York Department of Chemical and Materials Engineering, New Jersey Institute of Technology Newark College of Engineering, 161 Warren Street, Newark, New Jersey 07102, USA
| | - Anh Tong
- Otto H. York Department of Chemical and Materials Engineering, New Jersey Institute of Technology Newark College of Engineering, 161 Warren Street, Newark, New Jersey 07102, USA
| | - Mark Volosov
- Helen and John C. Hartmann Department of Electrical and Computer Engineering, New Jersey Institute of Technology Newark College of Engineering, Suite 200 University Heights, Newark, New Jersey 07102, USA
| | - Shreya Madhavarapu
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, New Jersey 08854, USA
| | - Joseph Freeman
- Department of Biomedical Engineering, Rutgers University, 599 Taylor Road, Piscataway, New Jersey 08854, USA
| | - Roman Voronov
- Author to whom correspondence should be addressed:. Tel.: +1 973 642 4762; Fax:+1 973 596 8436
| |
Collapse
|
5
|
Gonzalez-Suarez AM, Long A, Huang X, Revzin A. A Compact Control System to Enable Automated Operation of Microfluidic Bioanalytical Assays. BIOSENSORS 2022; 12:1160. [PMID: 36551127 PMCID: PMC9775492 DOI: 10.3390/bios12121160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
We describe a control system for operating valve-enabled microfluidic devices and leverage this control system to carry out a complex workflow of plasma separation from 8 μL of whole blood followed by on-chip mixing of plasma with assay reagents for biomarker detection. The control system incorporates pumps, digital pressure sensors, a microcontroller, solenoid valves and off-the-shelf components to deliver high and low air pressure in the desired temporal sequence to meter fluid flow and actuate microvalves. Importantly, our control system is portable, which is suitable for operating the microvalve-enabled microfluidic devices in the point-of-care setting.
Collapse
Affiliation(s)
| | - Alexander Long
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biology, St. Olaf College, Northfield, MN 55057, USA
| | - XuHai Huang
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Alexander Revzin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| |
Collapse
|
6
|
Tischler J, Swank Z, Hsiung HA, Vianello S, Lutolf MP, Maerkl SJ. An automated do-it-yourself system for dynamic stem cell and organoid culture in standard multi-well plates. CELL REPORTS METHODS 2022; 2:100244. [PMID: 35880022 PMCID: PMC9308133 DOI: 10.1016/j.crmeth.2022.100244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/25/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022]
Abstract
We present a low-cost, do-it-yourself system for complex mammalian cell culture under dynamically changing medium formulations by integrating conventional multi-well tissue culture plates with simple microfluidic control and system automation. We demonstrate the generation of complex concentration profiles, enabling the investigation of sophisticated input-response relations. We further apply our automated cell-culturing platform to the dynamic stimulation of two widely employed stem-cell-based in vitro models for early mammalian development: the conversion of naive mouse embryonic stem cells into epiblast-like cells and mouse 3D gastruloids. Performing automated medium-switch experiments, we systematically investigate cell fate commitment along the developmental trajectory toward mouse epiblast fate and examine symmetry-breaking, germ layer formation, and cardiac differentiation in mouse 3D gastruloids as a function of time-varying Wnt pathway activation. With these proof-of-principle examples, we demonstrate a highly versatile and scalable tool that can be adapted to specific research questions, experimental demands, and model systems.
Collapse
Affiliation(s)
- Julia Tischler
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
| | - Zoe Swank
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hao-An Hsiung
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
| | - Stefano Vianello
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
| | - Matthias P. Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
- Roche Institute for Translational Bioengineering (TB), Pharma Research and Early Development (pRED), F. Hoffman-La Roche Ltd, Basel, Switzerland
| | - Sebastian J. Maerkl
- Laboratory of Biological Network Characterization, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Vaud, Switzerland
| |
Collapse
|
7
|
Kehl F, Cretu VF, Willis PA. Open-source lab hardware: A versatile microfluidic control and sensor platform. HARDWAREX 2021; 10:e00229. [PMID: 35607658 PMCID: PMC9123481 DOI: 10.1016/j.ohx.2021.e00229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/23/2021] [Accepted: 09/02/2021] [Indexed: 05/25/2023]
Abstract
Here we describe a completely integrated and customizable microfluidic control and sensing architecture that can be readily implemented for laboratory or portable chemical or biological control and sensing applications. The compact platform enables control of 32 solenoid valves, a multitude of pumps and motors, a thermo-electric controller, a pressure controller, and a high voltage power supply. It also features two temperature probe interfaces, one relative humidity and ambient temperature sensor, two pressure sensors, and interfaces to an electrical conductivity sensor, flow sensor, and a bubble detector. The platform can be controlled via an onboard microcontroller and requires no proprietary software.
Collapse
Affiliation(s)
- Florian Kehl
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
- Innovation Cluster Space and Aviation (UZH Space Hub), Air Force Center, University of Zurich, 8600 Dübendorf, Switzerland
- Institute of Anatomy, Faculty of Medicine, University of Zurich, 8057 Zurich, Switzerland
- Institute of Medical Engineering, Space Biology Group, Lucerne University of Applied Sciences and Arts, 6052 Hergiswil, Switzerland
| | - Vlad F. Cretu
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - Peter A. Willis
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| |
Collapse
|
8
|
Markin CJ, Mokhtari DA, Sunden F, Appel MJ, Akiva E, Longwell SA, Sabatti C, Herschlag D, Fordyce PM. Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics. Science 2021; 373:373/6553/eabf8761. [PMID: 34437092 DOI: 10.1126/science.abf8761] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/24/2021] [Indexed: 12/21/2022]
Abstract
Systematic and extensive investigation of enzymes is needed to understand their extraordinary efficiency and meet current challenges in medicine and engineering. We present HT-MEK (High-Throughput Microfluidic Enzyme Kinetics), a microfluidic platform for high-throughput expression, purification, and characterization of more than 1500 enzyme variants per experiment. For 1036 mutants of the alkaline phosphatase PafA (phosphate-irrepressible alkaline phosphatase of Flavobacterium), we performed more than 670,000 reactions and determined more than 5000 kinetic and physical constants for multiple substrates and inhibitors. We uncovered extensive kinetic partitioning to a misfolded state and isolated catalytic effects, revealing spatially contiguous regions of residues linked to particular aspects of function. Regions included active-site proximal residues but extended to the enzyme surface, providing a map of underlying architecture not possible to derive from existing approaches. HT-MEK has applications that range from understanding molecular mechanisms to medicine, engineering, and design.
Collapse
Affiliation(s)
- C J Markin
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - D A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - F Sunden
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - M J Appel
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - E Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - S A Longwell
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - C Sabatti
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.,Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - D Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA. .,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - P M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. .,ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.,Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub; San Francisco, CA 94110, USA
| |
Collapse
|
9
|
Gao RZ, Ren CL. Synergizing microfluidics with soft robotics: A perspective on miniaturization and future directions. BIOMICROFLUIDICS 2021; 15:011302. [PMID: 33564346 PMCID: PMC7861881 DOI: 10.1063/5.0036991] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/19/2021] [Indexed: 05/12/2023]
Abstract
Soft robotics has gone through a decade of tremendous progress in advancing both fundamentals and technologies. It has also seen a wide range of applications such as surgery assistance, handling of delicate foods, and wearable assistive systems driven by its soft nature that is more human friendly than traditional hard robotics. The rapid growth of soft robotics introduces many challenges, which vary with applications. Common challenges include the availability of soft materials for realizing different functions and the precision and speed of control required for actuation. In the context of wearable systems, miniaturization appears to be an additional hurdle to be overcome in order to develop truly impactful systems with a high user acceptance. Microfluidics as a field of research has gone through more than two decades of intense and focused research resulting in many fundamental theories and practical tools that have the potentials to be applied synergistically to soft robotics toward miniaturization. This perspective aims to introduce the potential synergy between microfluidics and soft robotics as a research topic and suggest future directions that could leverage the advantages of the two fields.
Collapse
|
10
|
Aditham AK, Markin CJ, Mokhtari DA, DelRosso N, Fordyce PM. High-Throughput Affinity Measurements of Transcription Factor and DNA Mutations Reveal Affinity and Specificity Determinants. Cell Syst 2020; 12:112-127.e11. [PMID: 33340452 DOI: 10.1016/j.cels.2020.11.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/08/2020] [Accepted: 11/24/2020] [Indexed: 01/28/2023]
Abstract
Transcription factors (TFs) bind regulatory DNA to control gene expression, and mutations to either TFs or DNA can alter binding affinities to rewire regulatory networks and drive phenotypic variation. While studies have profiled energetic effects of DNA mutations extensively, we lack similar information for TF variants. Here, we present STAMMP (simultaneous transcription factor affinity measurements via microfluidic protein arrays), a high-throughput microfluidic platform enabling quantitative characterization of hundreds of TF variants simultaneously. Measured affinities for ∼210 mutants of a model yeast TF (Pho4) interacting with 9 oligonucleotides (>1,800 Kds) reveal that many combinations of mutations to poorly conserved TF residues and nucleotides flanking the core binding site alter but preserve physiological binding, providing a mechanism by which combinations of mutations in cis and trans could modulate TF binding to tune occupancies during evolution. Moreover, biochemical double-mutant cycles across the TF-DNA interface reveal molecular mechanisms driving recognition, linking sequence to function. A record of this paper's Transparent Peer Review process is included in the Supplemental Information.
Collapse
Affiliation(s)
- Arjun K Aditham
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Craig J Markin
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Daniel A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Nicole DelRosso
- Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94110, USA.
| |
Collapse
|
11
|
Goyal G, Elsbree N, Fero M, Hillson NJ, Linshiz G. Repurposing a microfluidic formulation device for automated DNA construction. PLoS One 2020; 15:e0242157. [PMID: 33175889 PMCID: PMC7657503 DOI: 10.1371/journal.pone.0242157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/27/2020] [Indexed: 11/19/2022] Open
Abstract
Microfluidic applications have expanded greatly over the past decade. For the most part, however, each microfluidics platform is developed with a specific task in mind, rather than as a general-purpose device with a wide-range of functionality. Here, we show how a microfluidic system, originally developed to investigate protein phase behavior, can be modified and repurposed for another application, namely DNA construction. We added new programable controllers to direct the flow of reagents across the chip. We designed the assembly of a combinatorial Golden Gate DNA library using TeselaGen DESIGN software and used the repurposed microfluidics platform to assemble the designed library from off-chip prepared DNA assembly pieces. Further experiments verified the sequences and function of the on-chip assembled DNA constructs.
Collapse
Affiliation(s)
- Garima Goyal
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Nick Elsbree
- TeselaGen Biotechnology, San Francisco, California, United States of America
| | - Michael Fero
- TeselaGen Biotechnology, San Francisco, California, United States of America
| | - Nathan J. Hillson
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Gregory Linshiz
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
| |
Collapse
|
12
|
Pearce JM. Economic savings for scientific free and open source technology: A review. HARDWAREX 2020; 8:e00139. [PMID: 32923748 PMCID: PMC7480774 DOI: 10.1016/j.ohx.2020.e00139] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 05/23/2023]
Abstract
Both the free and open source software (FOSS) as well as the distributed digital manufacturing of free and open source hardware (FOSH) has shown particular promise among scientists for developing custom scientific tools. Early research found substantial economic savings for these technologies, but as the open source design paradigm has grown by orders of magnitude it is possible that the savings observed in the early work was isolated to special cases. Today there are examples of open source technology for science in the vast majority of disciplines and several resources dedicated specifically to publishing them. Do the tremendous economic savings observed earlier hold today? To answer that question, this study evaluates free and open source technologies in the two repositories compared to proprietary functionally-equivalent tools as a function of their use of Arduino-based electronics, RepRap-class 3-D printing, as well as the combination of the two. The results of the review find overwhelming evidence for a wide range of scientific tools, that open source technologies provide economic savings of 87% compared to equivalent or lesser proprietary tools. These economic savings increased slightly to 89% for those that used Arduino technology and even more to 92% for those that used RepRap-class 3-D printing. Combining both Arduino and 3-D printing the savings averaged 94% for free and open source tools over commercial equivalents. The results provide strong evidence for financial support of open source hardware and software development for the sciences. Given the overwhelming economic advantages of free and open source technologies, it appears financially responsible to divert funding of proprietary scientific tools and their development in favor of FOSH. Policies were outlined that provide nations with a template for strategically harvesting the opportunities provided by the free and open source paradigm.
Collapse
Affiliation(s)
- Joshua M. Pearce
- Department of Materials Science and Engineering, Michigan Technological University, Houghton, MI 49931, USA
- Department of Electrical and Computer Engineering, Michigan Technological University, Houghton, MI 49931, USA
- Department of Electronics and Nanoengineering, School of Electrical Engineering, Aalto University, Espoo, Finland
| |
Collapse
|
13
|
Eggert S, Mieszczanek P, Meinert C, Hutmacher DW. OpenWorkstation: A modular open-source technology for automated in vitro workflows. HARDWAREX 2020; 8:e00152. [PMID: 35498237 PMCID: PMC9041211 DOI: 10.1016/j.ohx.2020.e00152] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 08/15/2020] [Accepted: 10/13/2020] [Indexed: 05/24/2023]
Abstract
Automation liberates scientific staff from repetitive tasks, decreases the probability of human error and consequently enhances the reproducibility of lab experiments. However, the use of laboratory automation in academic laboratories is limited due to high acquisition costs and the inability to customize off-the-shelf hardware. To address these challenges, we present an Open Source Hardware concept, referred to as OpenWorkstation, to build an assembly line-inspired platform consisting of ready-to-use and customizable modules. In contrast to current standalone solutions, the OpenWorkstation concept enables the combination of single hardware modules - each with a specific set of functionalities - to a modular workstation to provide a fully automated setup. The base setup consists of a pipetting and transport module and is designed to execute basic protocol steps for in vitro research applications, including pipetting operations for liquids and viscous substances and transportation of cell culture vessels between the modules. We demonstrate the successful application of this concept within a case study by the development of a storage module to facilitate high-throughput studies and a photo-crosslinker module to initiate photo-induced polymerization of hydrogel solutions. We present a Systems Engineering framework for customized module development, guidance for the design and assembly of the presented modules, and operational instructions on the usage of the workstation. By combining capabilities from various open source instrumentations into a modular technology platform, the OpenWorkstation concept will facilitate efficient and reliable experimentation for in vitro research. Ultimately, this concept will allow academic groups to improve replicability and reproducibility in cell culture process operations towards more economical and innovative research in the future.
Collapse
Affiliation(s)
- Sebastian Eggert
- Centre in Regenerative Medicine, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane 4000, QLD, Australia
- School of Mechanical, Medical and Process Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane 4000, QLD, Australia
- Chair of Medical Materials and Implants, Department of Mechanical Engineering and Munich School of BioEngineering, Technical University of Munich, Garching 85748, Germany
| | - Pawel Mieszczanek
- Centre in Regenerative Medicine, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane 4000, QLD, Australia
- School of Mechanical, Medical and Process Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane 4000, QLD, Australia
| | - Christoph Meinert
- Centre in Regenerative Medicine, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane 4000, QLD, Australia
- School of Mechanical, Medical and Process Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane 4000, QLD, Australia
| | - Dietmar W Hutmacher
- Centre in Regenerative Medicine, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane 4000, QLD, Australia
- School of Mechanical, Medical and Process Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane 4000, QLD, Australia
- ARC ITTC in Additive Biomanufacturing, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane 4000, QLD, Australia
| |
Collapse
|
14
|
A programmable epidermal microfluidic valving system for wearable biofluid management and contextual biomarker analysis. Nat Commun 2020; 11:4405. [PMID: 32879320 PMCID: PMC7467936 DOI: 10.1038/s41467-020-18238-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/12/2020] [Indexed: 11/08/2022] Open
Abstract
Active biofluid management is central to the realization of wearable bioanalytical platforms that are poised to autonomously provide frequent, real-time, and accurate measures of biomarkers in epidermally-retrievable biofluids (e.g., sweat). Accordingly, here, a programmable epidermal microfluidic valving system is devised, which is capable of biofluid sampling, routing, and compartmentalization for biomarker analysis. At its core, the system is a network of individually-addressable microheater-controlled thermo-responsive hydrogel valves, augmented with a pressure regulation mechanism to accommodate pressure built-up, when interfacing sweat glands. The active biofluid control achieved by this system is harnessed to create unprecedented wearable bioanalytical capabilities at both the sensor level (decoupling the confounding influence of flow rate variability on sensor response) and the system level (facilitating context-based sensor selection/protection). Through integration with a wireless flexible printed circuit board and seamless bilateral communication with consumer electronics (e.g., smartwatch), contextually-relevant (scheduled/on-demand) on-body biomarker data acquisition/display was achieved. Wearable biosensors have been used successfully for biomarker analysis, however, a lack of control over sampling limits applications. Here, the authors report a programmable microfluidic valve to control flow rate, sampling times and allow for biofluid routing and compartmentalisation.
Collapse
|
15
|
Gao RZ, Hébert M, Huissoon J, Ren CL. µPump: An open-source pressure pump for precision fluid handling in microfluidics. HARDWAREX 2020; 7:e00096. [PMID: 35495202 PMCID: PMC9041173 DOI: 10.1016/j.ohx.2020.e00096] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/19/2019] [Accepted: 01/06/2020] [Indexed: 05/21/2023]
Abstract
An open-source precision pressure pump system and control software is presented, primarily designed for the experimental microfluidics community, although others may find additional uses for this precision pressure source. This mechatronic system is coined 'µPump,' and its performance rivals that of commercially available systems, at a fraction of the cost. The pressure accuracy, stability, and resolution are 0.09%, 0.02%, and 0.02% of the full span, respectively. The settling time to reach 2 bar from zero and stabilize is less than 2 s. Material for building a four-channel µPump (approx. $3000 USD) or an eight-channel µPump (approx. $5000 USD) is approximately a quarter, or a third of the cost of buying a high-end commercial system, respectively. The design rationale is presented, together with documented design details and software, so that the system may be replicated or customized to particular applications. µPump can be used for two-phase droplet microfluidics, single-phase microfluidics, gaseous flow microfluidics and any other applications requiring precise fluid handling. µPump provides researchers, students, and startups with a cost-effective solution for precise fluid control.
Collapse
|
16
|
Tong A, Pham QL, Shah V, Naik A, Abatemarco P, Voronov R. Automated Addressable Microfluidic Device for Minimally Disruptive Manipulation of Cells and Fluids within Living Cultures. ACS Biomater Sci Eng 2020; 6:1809-1820. [DOI: 10.1021/acsbiomaterials.9b01969] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Anh Tong
- Otto H. York Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark College of Engineering, 161 Warren Street, Newark, New Jersey 07102, United States
| | - Quang Long Pham
- Otto H. York Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark College of Engineering, 161 Warren Street, Newark, New Jersey 07102, United States
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, Massachusetts 02155, United States
| | - Vatsal Shah
- Department of Computer Science, Ying Wu College of Computing Sciences, New Jersey Institute of Technology, Newark College of Engineering, Suite 3500, University Heights, Newark, New Jersey 07102, United States
- Federated Department of Mechanical and Industrial Engineering, New Jersey Institute of Technology, Newark College of Engineering, Suite 204, University Heights, Newark, New Jersey 07102, United States
| | - Akshay Naik
- Helen and John C. Hartmann Department of Electrical and Computer Engineering, New Jersey Institute of Technology, Newark College of Engineering, Suite 200, University Heights, Newark, New Jersey 07102, United States
| | - Paul Abatemarco
- Otto H. York Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark College of Engineering, 161 Warren Street, Newark, New Jersey 07102, United States
| | - Roman Voronov
- Otto H. York Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark College of Engineering, 161 Warren Street, Newark, New Jersey 07102, United States
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark College of Engineering, 323 Dr. Martin Luther King Jr. Boulevard, Newark, New Jersey 07103, United States
| |
Collapse
|
17
|
Longwell SA, Fordyce PM. micrIO: an open-source autosampler and fraction collector for automated microfluidic input-output. LAB ON A CHIP 2020; 20:93-106. [PMID: 31701110 PMCID: PMC6923132 DOI: 10.1039/c9lc00512a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Microfluidic devices are an enabling technology for many labs, facilitating a wide range of applications spanning high-throughput encapsulation, molecular separations, and long-term cell culture. In many cases, however, their utility is limited by a 'world-to-chip' barrier that makes it difficult to serially interface samples with these devices. As a result, many researchers are forced to rely on low-throughput, manual approaches for managing device input and output (IO) of samples, reagents, and effluent. Here, we present a hardware-software platform for automated microfluidic IO (micrIO). The platform, which is uniquely compatible with positive-pressure microfluidics, comprises an 'AutoSipper' for input and a 'Fraction Collector' for output. To facilitate widespread adoption, both are open-source builds constructed from components that are readily purchased online or fabricated from included design files. The software control library, written in Python, allows the platform to be integrated with existing experimental setups and to coordinate IO with other functions such as valve actuation and assay imaging. We demonstrate these capabilities by coupling both the AutoSipper and Fraction Collector to two microfluidic devices: a simple, valved inlet manifold and a microfluidic droplet generator that produces beads with distinct spectral codes. Analysis of the collected materials in each case establishes the ability of the platform to draw from and output to specific wells of multiwell plates with negligible cross-contamination between samples.
Collapse
Affiliation(s)
- Scott A Longwell
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA, USA. and Department of Genetics, Stanford University, Stanford, CA, USA and ChEM-H Institute, Stanford University, Stanford, CA, USA and Chan Zuckerberg Biohub, San Francisco, CA, USA
| |
Collapse
|
18
|
Abstract
A wide range of medical devices have significant electronic components. Compared to open-source medical software, open (and open-source) electronic hardware has been less published in peer-reviewed literature. In this review, we explore the developments, significance, and advantages of using open platform electronic hardware for medical devices. Open hardware electronics platforms offer not just shorter development times, reduced costs, and customization; they also offer a key potential advantage which current commercial medical devices lack—seamless data sharing for machine learning and artificial intelligence. We explore how various electronic platforms such as microcontrollers, single board computers, field programmable gate arrays, development boards, and integrated circuits have been used by researchers to design medical devices. Researchers interested in designing low cost, customizable, and innovative medical devices can find references to various easily available electronic components as well as design methodologies to integrate those components for a successful design.
Collapse
|
19
|
Zhu B, Hsieh YP, Murphy TW, Zhang Q, Naler LB, Lu C. MOWChIP-seq for low-input and multiplexed profiling of genome-wide histone modifications. Nat Protoc 2019; 14:3366-3394. [PMID: 31666743 DOI: 10.1038/s41596-019-0223-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 06/27/2019] [Indexed: 01/11/2023]
Abstract
Epigenetic mechanisms such as histone modifications play critical roles in adaptive tuning of chromatin structures. Profiling of various histone modifications at the genome scale using tissues from animal and human samples is an important step for functional studies of epigenomes and epigenomics-based precision medicine. Because the profile of a histone mark is highly specific to a cell type, cell isolation from tissues is often necessary to generate a homogeneous cell population, and such operations tend to yield a low number of cells. In addition, high-throughput processing is often desirable because of the multiplexity of histone marks of interest and the large quantity of samples in a hospital setting. In this protocol, we provide detailed instructions for device fabrication, setup, and operation of microfluidic oscillatory washing-based chromatin immunoprecipitation followed by sequencing (MOWChIP-seq) for profiling of histone modifications using as few as 100 cells per assay with a throughput as high as eight assays in one run. MOWChIP-seq operation involves flowing of chromatin fragments through a packed bed of antibody-coated beads, followed by vigorous microfluidic oscillatory washing. Our process is semi-automated to reduce labor and improve reproducibility. Using one eight-unit device, it takes 2 d to produce eight sequencing libraries from chromatin samples. The technology is scalable. We used the protocol to study a number of histone modifications in various types of mouse and human tissues. The protocol can be conducted by a user who is familiar with molecular biology procedures and has basic engineering skills.
Collapse
Affiliation(s)
- Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Yuan-Pang Hsieh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Travis W Murphy
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Qiang Zhang
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA.
| |
Collapse
|
20
|
Abstract
We present a fully-integrated solution for controlling pneumatically-driven microfluidic chips, featuring a pump, one or more pressure regulators and up to 32 solenoid valves, controlled by a microcontroller. The microfluidics control system requires only a power source and a computer or mobile device for its operation. A touchscreen interface communicates with the microcontroller over USB or Bluetooth and allows users to control the system with ease either manually or autonomously, allowing experiments to run with no user intervention. The pressure regulators were purpose-built, enabling integrated pressure sources on-board, rather than relying on external equipment. These regulators can also be used as stand-alone devices in any other application.
Collapse
|
21
|
Chang JC, Swank Z, Keiser O, Maerkl SJ, Amstad E. Microfluidic device for real-time formulation of reagents and their subsequent encapsulation into double emulsions. Sci Rep 2018; 8:8143. [PMID: 29802303 PMCID: PMC5970246 DOI: 10.1038/s41598-018-26542-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/11/2018] [Indexed: 01/04/2023] Open
Abstract
Emulsion drops are often employed as picoliter-sized containers to perform screening assays. These assays usually entail the formation of drops encompassing discrete objects such as cells or microparticles and reagents to study interactions between the different encapsulants. Drops are also used to screen influences of reagent concentrations on the final product. However, these latter assays are less frequently performed because it is difficult to change the reagent concentration over a wide range and with high precision within a single experiment. In this paper, we present a microfluidic double emulsion drop maker containing pneumatic valves that enable real-time formulation of different reagents using pulse width modulation and consequent encapsulation of the mixed solutions. This device can produce drops from reagent volumes as low as 10 µL with minimal sample loss, thereby enabling experiments that would be prohibitively expensive using drop generators that do not contain valves. We employ this device to monitor the kinetics of the cell-free synthesis of green fluorescent proteins inside double emulsions. To demonstrate the potential of this device for real-time formulation, we perform DNA titration experiments to test the influence of DNA concentration on the amount of green fluorescence protein produced in double emulsions by a coupled cell-free transcription / translation system.
Collapse
Affiliation(s)
- Jui-Chia Chang
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Zoe Swank
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Oliver Keiser
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sebastian J Maerkl
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Esther Amstad
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| |
Collapse
|
22
|
Abstract
Microfluidic devices with integrated valves provide precise, programmable fluid handling platforms for high-throughput biological or chemical assays. However, setting up the infrastructure to control such platforms often requires specific engineering expertise or expensive commercial solutions. To address these obstacles, we present a Kit for Arduino-based Transistor Array Actuation (KATARA), an open-source and low-cost Arduino-based controller that can drive 70 solenoid valves to pneumatically actuate integrated microfluidic valves. We include a python package with a GUI to control the KATARA from a personal computer. No programming experience is required.
Collapse
Affiliation(s)
- Jonathan A. White
- Department of Bioengineering University of California, Berkeley, CA 94720,
United States
| | - Aaron M. Streets
- Department of Bioengineering University of California, Berkeley, CA 94720,
United States
- Chan Zuckerberg Biohub, San Francisco, CA 94158, United States
- Corresponding author at: Department of Bioengineering University
of California, Berkeley, CA 94720, United States.
(A.M. Streets)
| |
Collapse
|
23
|
Aditham AK, Shimko TC, Fordyce PM. BET-seq: Binding energy topographies revealed by microfluidics and high-throughput sequencing. Methods Cell Biol 2018; 148:229-250. [PMID: 30473071 PMCID: PMC7531582 DOI: 10.1016/bs.mcb.2018.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Biophysical models of transcriptional regulation rely on energetic measurements of the binding affinities between transcription factors (TFs) and target DNA binding sites. Historically, assays capable of measuring TF-DNA binding affinities have been relatively low-throughput (measuring ~103 sequences in parallel) and have required significant specialized equipment, limiting their use to a handful of laboratories. Recently, we developed an experimental assay and analysis pipeline that allows measurement of binding energies between a single TF and up to 106 DNA species in a single experiment (Binding Energy Topography by sequencing, or BET-seq) (Le et al., 2018). BET-seq employs the Mechanically Induced Trapping of Molecular Interactions (MITOMI) platform to purify DNA bound to a TF at equilibrium followed by high coverage sequencing to reveal relative differences in binding energy for each sequence. While we have previously used BET-seq to refine the binding affinity landscapes surrounding high-affinity DNA consensus target sites, we anticipate this technique will be applied in future work toward measuring a wide variety of TF-DNA landscapes. Here, we provide detailed instructions and general considerations for DNA library design, performing BET-seq assays, and analyzing the resulting data.
Collapse
Affiliation(s)
- Arjun K. Aditham
- Department of Bioengineering, Stanford University, Stanford, CA, United States,Stanford ChEM-H, Stanford University, Stanford, CA, United States
| | - Tyler C. Shimko
- Department of Genetics, Stanford University, Stanford, CA, United States
| | - Polly M. Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA, United States,Stanford ChEM-H, Stanford University, Stanford, CA, United States,Department of Genetics, Stanford University, Stanford, CA, United States,Chan Zuckerberg Biohub, San Francisco, CA, United States,Corresponding author:
| |
Collapse
|