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Lentimpra and Mpraflow for High-Throughput Functional
PROTOCOL https://doi.org/10.1038/s41596-020-0333-5 lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements ✉ M. Grace Gordon 1,2,3,16, Fumitaka Inoue 1,2,16 , Beth Martin4,16, Max Schubach 5,6,16, Vikram Agarwal4,7, Sean Whalen8, Shiyun Feng1,2, Jingjing Zhao1,2, Tal Ashuach9, Ryan Ziffra1,2, 1,2,9 1,2 9,10 1,2,10,11,12 Anat Kreimer , Ilias Georgakopoulous-Soares✉, Nir Yosef , Chun✉ Jimmie Ye , ✉ Katherine S. Pollard2,8,10,13, Jay Shendure 4,14,15 , Martin Kircher 5,6 and Nadav Ahituv 1,2 Massively parallel reporter assays (MPRAs) can simultaneously measure the function of thousands of candidate regulatory sequences (CRSs) in a quantitative manner. In this method, CRSs are cloned upstream of a minimal promoter and reporter gene, alongside a unique barcode, and introduced into cells. If the CRS is a functional regulatory element, it will lead to the transcription of the barcode sequence, which is measured via RNA sequencing and normalized for cellular integration via DNA sequencing of the barcode. This technology has been used to test thousands of sequences and their variants for regulatory activity, to decipher the regulatory code and its evolution, and to develop genetic switches. Lentivirus-based MPRA (lentiMPRA) produces ‘in-genome’ readouts and enables the use of this technique in hard-to- 1234567890():,; 1234567890():,; transfect cells. Here, we provide a detailed protocol for lentiMPRA, along with a user-friendly Nextflow-based computational pipeline—MPRAflow—for quantifying CRS activity from different MPRA designs. The lentiMPRA protocol takes ~2 months, which includes sequencing turnaround time and data processing with MPRAflow.
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Preparation and Implementation of Optofluidic Neural Probes for in Vivo
PROTOCOL EXTENSION Preparation and implementation of optofluidic neural probes for in vivo wireless pharmacology and optogenetics Jordan G McCall1–4, Raza Qazi5, Gunchul Shin6, Shuo Li6,14, Muhammad Hamza Ikram7, Kyung-In Jang6,8, Yuhao Liu6, Ream Al-Hasani1–4, Michael R Bruchas1–4,9,13, Jae-Woong Jeong5,7,13 & John A Rogers6,10–13 1Department of Anesthesiology, Division of Basic Research, Washington University School of Medicine, St. Louis, Missouri, USA. 2Washington University Pain Center, Washington University School of Medicine, St. Louis, Missouri, USA. 3Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, USA. 4Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri, USA. 5Department of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Colorado, USA. 6Department of Materials Science and Engineering, Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. 7Materials Science and Engineering Program, University of Colorado Boulder, Colorado, USA. 8Department of Robotics Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea. 9Department of Biomedical Engineering, Washington University, St. Louis, Missouri, USA. 10Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. 11Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. 12Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. 13These authors contributed equally to this work. 14Present address: Department of Materials Science and Engineering, Cornell University, New York, USA. Correspondence should be addressed to M.R.B. ([email protected]), J.-W.J. ([email protected]), or J.A.R.
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Network‐Based Approaches for Pathway Level Analysis
Network-Based Approaches for Pathway UNIT 8.25 Level Analysis Tin Nguyen,1 Cristina Mitrea,2 and Sorin Draghici2,3 1Department of Computer Science and Engineering, University of Nevada, Reno, Nevada 2Department of Computer Science, Wayne State University, Detroit, Michigan 3Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan Identification of impacted pathways is an important problem because it allows us to gain insights into the underlying biology beyond the detection of differ- entially expressed genes. In the past decade, a plethora of methods have been developed for this purpose. The last generation of pathway analysis methods are designed to take into account various aspects of pathway topology in order to increase the accuracy of the findings. Here, we cover 34 such topology-based pathway analysis methods published in the past 13 years. We compare these methods on categories related to implementation, availability, input format, graph models, and statistical approaches used to compute pathway level statis- tics and statistical significance. We also discuss a number of critical challenges that need to be addressed, arising both in methodology and pathway repre- sentation, including inconsistent terminology, data format, lack of meaningful benchmarks, and, more importantly, a systematic bias that is present in most existing methods. C 2018 by John Wiley & Sons, Inc. Keywords: systems biology r pathway r topology r gene network r survey r pathway analysis How to cite this article: Nguyen, T., Mitrea, C., & Draghici, S. (2018). Network-based approaches for pathway level analysis. Current Protocols in Bioinformatics, 61, 8.25.1–8.25.24. doi: 10.1002/cpbi.42 INTRODUCTION this gap is the fact that living organisms are With rapid advances in high-throughput complex systems whose emerging phenotypes technologies, various kinds of genomic are the results of multiple complex interactions data have become prevalent in most of taking place on various metabolic and signal- biomedical research.
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Detecting Ultralow-Frequency Mutations by Duplex Sequencing
PROTOCOL Detecting ultralow-frequency mutations by Duplex Sequencing Scott R Kennedy1, Michael W Schmitt2, Edward J Fox1, Brendan F Kohrn3, Jesse J Salk2, Eun Hyun Ahn1, Marc J Prindle1, Kawai J Kuong1, Jiang-Cheng Shen1, Rosa-Ana Risques1 & Lawrence A Loeb1,4 1Department of Pathology, University of Washington, Seattle, USA. 2Department of Medicine, University of Washington, Seattle, USA. 3Department of Biology, Portland State University, Portland, Oregon, USA. 4Department of Biochemistry, University of Washington, Seattle, USA. Correspondence should be addressed to L.A.L. ([email protected]). Published online 9 October 2014; corrected online 22 October 2014 (details online); doi:10.1038/nprot.2014.170 Duplex Sequencing (DS) is a next-generation sequencing methodology capable of detecting a single mutation among >1 × 107 wild-type nucleotides, thereby enabling the study of heterogeneous populations and very-low-frequency genetic alterations. DS can be applied to any double-stranded DNA sample, but it is ideal for small genomic regions of <1 Mb in size. The method relies on the ligation of sequencing adapters harboring random yet complementary double-stranded nucleotide sequences to the sample DNA of interest. Individually labeled strands are then PCR-amplified, creating sequence ‘families’ that share a common tag sequence derived from the two original complementary strands. Mutations are scored only if the variant is present in the PCR families arising from both of the two DNA strands. Here we provide a detailed protocol for efficient DS adapter synthesis, library preparation and target enrichment, as well as an overview of the data analysis workflow. The protocol typically takes 1–3 d.
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Shao-Shan Carol Huang 12 Waverly Pl, New York, NY 10003 Curriculum Vitae  Huanglab.Rbind.Io  +1 212 998 8286
Center for Genomics and Systems Biology Department of Biology, New York University Shao-shan Carol Huang 12 Waverly Pl, New York, NY 10003 Curriculum Vitae huanglab.rbind.io +1 212 998 8286 [email protected] April 2020 @shhuang1 hlab1 Education and qualifications 2018 Workshop on Leadership in Biosciences Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. 2011 Ph.D., Computational and Systems Biology Massachusetts Institute of Technology, Cambridge, MA, USA Advisor: Dr. Ernest Fraenkel Thesis: A constraint optimization framework for discovery of cellular signaling and regulatory networks 2005 B.Sc., Combined Honors Computer Science and Biology, Co-op Option University of British Columbia, Vancouver, BC, Canada Advisor: Dr. Wyeth Wasserman Honors thesis: Computational identification of over-represented combinations of transcription factor binding sites in sets of co-expressed genes Current position 2019- Affiliate Faculty, Center for Data Science, New York University 2018- Assistant Professor, Center for Genomics and Systems Biology, Department of Biology, New York University Past research positions 2011-2017 Postdoctoral associate, Genomic Analysis Laboratory & Plant Biology Laboratory The Salk Institute for Biological Studies Advisor: Dr. Joseph Ecker 2011 Postdoctoral associate, Department of Biological Engineering Massachusetts Institute of Technology Advisor: Dr. Ernest Fraenkel 2005-2011 Graduate student, Program in Computational and Systems Biology Massachusetts Institute of Technology Advisor: Dr. Ernest Fraenkel 2004-2005
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Fluorine-19 Nuclear Magnetic Resonance of Chimeric Antigen Receptor T Cell Biodistribution in Murine Cancer Model
UCSF UC San Francisco Previously Published Works Title Fluorine-19 nuclear magnetic resonance of chimeric antigen receptor T cell biodistribution in murine cancer model. Permalink https://escholarship.org/uc/item/8v82b8b2 Journal Scientific reports, 7(1) ISSN 2045-2322 Authors Chapelin, Fanny Gao, Shang Okada, Hideho et al. Publication Date 2017-12-18 DOI 10.1038/s41598-017-17669-4 Peer reviewed eScholarship.org Powered by the California Digital Library University of California www.nature.com/scientificreports OPEN Fluorine-19 nuclear magnetic resonance of chimeric antigen receptor T cell biodistribution in Received: 5 June 2017 Accepted: 28 November 2017 murine cancer model Published: xx xx xxxx Fanny Chapelin1, Shang Gao2, Hideho Okada3,4, Thomas G. Weber2, Karen Messer5 & Eric T. Ahrens2 Discovery of efective cell therapies against cancer can be accelerated by the adaptation of tools to rapidly quantitate cell biodistribution and survival after delivery. Here, we describe the use of nuclear magnetic resonance (NMR) ‘cytometry’ to quantify the biodistribution of immunotherapeutic T cells in intact tissue samples. In this study, chimeric antigen receptor (CAR) T cells expressing EGFRvIII targeting transgene were labeled with a perfuorocarbon (PFC) emulsion ex vivo and infused into immunocompromised mice bearing subcutaneous human U87 glioblastomas expressing EGFRvIII and luciferase. Intact organs were harvested at day 2, 7 and 14 for whole-sample fuorine-19 (19F) NMR to quantitatively measure the presence of PFC-labeled CAR T cells, followed by histological validation. NMR measurements showed greater CAR T cell homing and persistence in the tumors and spleen compared to untransduced T cells. Tumor growth was monitored with bioluminescence imaging, showing that CAR T cell treatment resulted in signifcant tumor regression compared to untransduced T cells.
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Real-Time MRI-Guided Catheter Tracking Using Hyperpolarized Silicon Particles
Rowan University Rowan Digital Works Faculty Scholarship for the College of Science & Mathematics College of Science & Mathematics 1-10-2015 Real-Time MRI-Guided Catheter Tracking Using Hyperpolarized Silicon Particles Nicholas Whiting Rowan University Jingzhe Hu University of Texas MD Anderson Cancer Center Jay Shah University of Texas MD Anderson Cancer Center Maja Cassidy Delft University of Technology Erik Cressman University of Minnesota See next page for additional authors Follow this and additional works at: https://rdw.rowan.edu/csm_facpub Part of the Materials Science and Engineering Commons, Medical Biophysics Commons, and the Radiology Commons Recommended Citation Whiting, N., Hu, J., Shah, J. V., Cassidy, M. C., Cressman, E., Millward, N. Z., ... Bhattacharya, P. K. (2015). Real-Time MRI-Guided Catheter Tracking Using Hyperpolarized Silicon Particles. Scientific Reports, 5, [12842]. DOI: 10.1038/srep12842. This Article is brought to you for free and open access by the College of Science & Mathematics at Rowan Digital Works. It has been accepted for inclusion in Faculty Scholarship for the College of Science & Mathematics by an authorized administrator of Rowan Digital Works. Authors Nicholas Whiting, Jingzhe Hu, Jay Shah, Maja Cassidy, Erik Cressman, Niki Millward, David Menter, Charles Marcus, and Pratip Bhattacharya This article is available at Rowan Digital Works: https://rdw.rowan.edu/csm_facpub/104 www.nature.com/scientificreports OPEN Real-Time MRI-Guided Catheter Tracking Using Hyperpolarized Silicon Particles Received: 11 March 2015 1,* 1,2,* 1,3 4 5 Accepted: 13 July 2015 Nicholas Whiting , Jingzhe Hu , Jay V. Shah , Maja C. Cassidy , Erik Cressman , 1 6 7 1 Published: 04 August 2015 Niki Zacharias Millward , David G.
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A Robust Unsupervised Machine-Learning Method to Quantify the Morphological Heterogeneity of Cells and Nuclei
PROTOCOL https://doi.org/10.1038/s41596-020-00432-x A robust unsupervised machine-learning method to quantify the morphological heterogeneity of cells and nuclei 1,2,6 1,6 1 1,3,4,5✉ Jude M. Phillip ✉ , Kyu-Sang Han , Wei-Chiang Chen , Denis Wirtz and Pei-Hsun Wu 1 Cell morphology encodes essential information on many underlying biological processes. It is commonly used by clinicians and researchers in the study, diagnosis, prognosis, and treatment of human diseases. Quantification of cell morphology has seen tremendous advances in recent years. However, effectively defining morphological shapes and evaluating the extent of morphological heterogeneity within cell populations remain challenging. Here we present a protocol and software for the analysis of cell and nuclear morphology from fluorescence or bright-field images using the VAMPIRE algorithm (https://github.com/kukionfr/VAMPIRE_open). This algorithm enables the profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Examining the distributions of cell morphologies across automatically identified shape modes provides an effective visualization scheme that relates cell shapes to cellular subtypes based on endogenous and exogenous cellular conditions. In addition, these shape mode 1234567890():,; 1234567890():,; distributions offer a direct and quantitative way to measure the extent of morphological heterogeneity within cell populations. This protocol is highly automated and fast, with the ability to quantify the morphologies from 2D projections of cells seeded both on 2D substrates or embedded within 3D microenvironments, such as hydrogels and tissues. The complete analysis pipeline can be completed within 60 minutes for a dataset of ~20,000 cells/2,400 images.
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Genetonic: an R/Bioconductor Package for Streamlining the Interpretation of RNA-Seq Data
bioRxiv preprint doi: https://doi.org/10.1101/2021.05.19.444862; this version posted May 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data Federico Marini1,2,*, Annekathrin Ludt1, Jan Linke1,2, and Konstantin Strauch1 1Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Germany 2Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg-University Mainz, Germany. *To whom correspondence should be addressed ([email protected]) May 19, 2021 Abstract Background: The interpretation of results from transcriptome profiling experiments via RNA sequencing (RNA-seq) can be a complex task, where the essential information is distributed among different tabular and list formats - normalized expression values, results from differential expression analysis, and results from functional enrichment analyses. A number of tools and databases are widely used for the purpose of identification of relevant functional patterns, yet often their contextualization within the data and results at hand is not straightforward, especially if these analytic components are not combined together efficiently. Results: We developed the GeneTonic software package, which serves as a comprehensive toolkit for streamlining the interpretation of functional enrichment analyses, by fully leveraging the information of expression values in a differential expression context. GeneTonic is implemented in R and Shiny, leveraging packages that enable HTML-based interactive visualizations for executing drilldown tasks seamlessly, viewing the data at a level of increased detail.
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Is a Tool Kit to Assess the Dynamics of Glioma
TOOLS AND RESOURCES Correlated magnetic resonance imaging and ultramicroscopy (MR-UM) is a tool kit to assess the dynamics of glioma angiogenesis Michael O Breckwoldt1,2*†, Julia Bode3,4†, Felix T Kurz1, Angelika Hoffmann1, Katharina Ochs2,4, Martina Ott2,5, Katrin Deumelandt2,5, Thomas Kru¨ wel6, Daniel Schwarz1, Manuel Fischer1, Xavier Helluy1,7, David Milford1, Klara Kirschbaum1, Gergely Solecki5, Sara Chiblak8,9,10, Amir Abdollahi8,9,10, Frank Winkler5, Wolfgang Wick5,11, Michael Platten2,5, Sabine Heiland1, Martin Bendszus1†, Bjo¨ rn Tews3,4*† 1Neuroradiology Department, University Hospital Heidelberg, Heidelberg, Germany; 2Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany; 3Schaller Research Group, University of Heidelberg and German Cancer Research Center, Heidelberg, Germany; 4Molecular Mechanisms of Tumor Invasion, German Cancer Research Center, Heidelberg, Germany; 5Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany; 6Department of Diagnostic and Interventional Radiology, University Medical Center Go¨ ttingen, Go¨ ttingen, Germany; 7NeuroImaging Centre, Research Department of Neuroscience, Ruhr-University Bochum, Bochum, Germany; 8German Cancer *For correspondence: michael. Consortium and Heidelberg Institute of Radiation Oncology, National Center for [email protected]. Radiation Research in Oncology, Heidelberg, Germany; 9Heidelberg University de (MOB); b.tews@dkfz- School of Medicine,
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Npgrj Nprot 2007-073 715..726
PROTOCOL Determining the stoichiometry and interactions of macromolecular assemblies from mass spectrometry Helena Hernańdez & Carol V Robinson Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, UK. Correspondence should be addressed to C.V.R. ([email protected]). Published online 22 March 2007; doi:10.1038/nprot.2007.73 The growing number of applications to determine the stoichiometry, interactions and even subunit architecture of protein complexes from mass spectra suggests that some general guidelines can now be proposed. In this protocol, we describe the necessary steps s required to maintain interactions between subunits in the gas phase. We begin with the preparation of suitable solutions for electrospray (ES) and then consider the transmission of complexes through the various stages of the mass spectrometer until their detection. Subsequent steps are also described, including the dissociation of these complexes into multiple subcomplexes for generation of interaction networks. Throughout we highlight the critical experimental factors that determine success. Overall, we develop a generic protocol that can be carried out using commercially available ES mass spectrometers without extensive modification. natureprotocol / m o c INTRODUCTION . e r The essential role of mass spectrometry (MS) coupled with the soft (ii) To determine the relative binding strength and topology. u t a ionization processes of either matrix-assisted laser desorption MS/MS experiments can indicate which subunits are on the periph- n . 7 w (MALDI) or electrospray (ES) ionization in the field of proteomics ery of a complex as they are in general the most readily dissociated . w 1 w is well established . Alongside these developments for proteomics, ES (iii) To identify protein–protein contacts.
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Wang, L., and Tsien, R.Y
PROTOCOL Evolving proteins in mammalian cells using somatic hypermutation Lei Wang1 & Roger Y Tsien2 1The Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, USA. 2Departments of Pharmacology and Chemistry and Biochemistry, Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Dr., La Jolla, California 92093-0647, USA. Correspondence should be addressed to L.W. ([email protected]). Published online 26 October 2006; doi:10.1038/nprot.2006.243 s We describe a new method to mutate target genes through somatic hypermutation (SHM) and to evolve proteins directly in living mammalian cells. Target genes are expressed under the control of an inducible promoter in a B-cell line that hypermutates its immunoglobulin (Ig) V genes constitutively. Mutations can be introduced into the target gene through SHM upon transcription. Mutant genes are then expressed and selected or screened for desired properties in cells. Identiﬁed cells are subjected to another round of mutation and selection or screening. This process can be iterated easily for numerous rounds, and multiple reinforcing natureprotocol / mutations can be accumulated to produce desirable phenotypes. This approach bypasses labor-intensive in vitro mutagenesis and m o samples a large protein sequence space. In this protocol a monomeric red ﬂuorescent protein (mRFP1.2) was evolved in Ramos cells c . e to afford a mutant (mPlum) with far-red emission. This method can be adapted to evolve other eukaryotic proteins and to be used in r u B B t other cells able to perform SHM.
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