Summit: Automated Analysis of Arrayed Single-Cell Gel Electrophoresis

Toby, 2016, Progress in Top-Down Proteomics and the Analysis of Proteoforms, Annu. Rev. Anal. Chem., 9, 499, 10.1146/annurev-anchem-071015-041550 Burnette, 1981, “Western Blotting”: Electrophoretic Transfer of Proteins from Sodium Dodecyl Sulfate-Polyacrylamide Gels to Unmodified Nitrocellulose and Radiographic Detection with Antibody and Radioiodinated Protein A, Anal. Biochem., 112, 195, 10.1016/0003-2697(81)90281-5 Wenisch, 1993, Conventional Isoelectric Focusing and Immobilized PH Gradients in ‘Macroporous’ Polyacrylamide Gels, Electrophoresis, 14, 583, 10.1002/elps.1150140192 Righetti, 1976, Isoelectric Points and Molecular Weights of Proteins, J. Chromatogr. A, 127, 1, 10.1016/S0021-9673(00)98537-6 Herr, 2004, Photopolymerized Cross-Linked Polycrylamide Gels for On-Chip Protein Sizing, Anal. Chem., 76, 4727, 10.1021/ac049686u Jin, 2016, Multiplexed Western Blotting Using Microchip Electrophoresis, Anal. Chem., 88, 6703, 10.1021/acs.analchem.6b00705 Anderson, 2011, Western Blotting Using Capillary Electrophoresis, Anal. Chem., 83, 1350, 10.1021/ac102671n Bharadwaj, 2002, Design and Optimization of On-Chip Capillary Electrophoresis, Electrophoresis, 23, 2729, 10.1002/1522-2683(200208)23:16<2729::AID-ELPS2729>3.0.CO;2-I Mellors, 2010, Integrated Microfluidic Device for Automated Single Cell Analysis Using Electrophoretic Separation and Electrospray Ionization Mass Spectrometry, Anal. Chem., 82, 967, 10.1021/ac902218y Gassmann, 2009, Quantifying Western Blots: Pitfalls of Densitometry, Electrophoresis, 30, 1845, 10.1002/elps.200800720 Duncombe, 2013, Photopatterned Free-Standing Polyacrylamide Gels for Microfluidic Protein Electrophoresis, Lab Chip, 13, 2115, 10.1039/c3lc50269d Pan, 2016, Determination of Equilibrium Dissociation Constants for Recombinant Antibodies by High-Throughput Affinity Electrophoresis, Sci. Rep., 6, 39774, 10.1038/srep39774 Hughes, 2014, Single-Cell Western Blotting, Nat. Methods, 11, 749, 10.1038/nmeth.2992 Gutzweiler, 2017, Open Microfluidic Gel Electrophoresis: Rapid and Low Cost Separation and Analysis of DNA at the Nanoliter Scale, Electrophoresis, 38, 1764, 10.1002/elps.201700001 Wood, 2010, Single Cell Trapping and DNA Damage Analysis Using Microwell Arrays, Proc. Natl. Acad. Sci. U.S.A., 107, 10008, 10.1073/pnas.1004056107 Tentori, 2016, Detection of Isoforms Differing by a Single Charge Unit in Individual Cells, Angew. Chem. Int. Ed., 55, 12431, 10.1002/anie.201606039 Shackman, 2004, High-Throughput Automated Post-Processing of Separation Data, J. Chromatogr. A, 1040, 273, 10.1016/j.chroma.2004.04.004 Weingeist, 2013, Single-Cell Microarray Enables High-Throughput Evaluation of DNA Double-Strand Breaks and DNA Repair Inhibitors, Cell Cycle, 12, 907, 10.4161/cc.23880 Ngo, 2020, Sensitive CometChip Assay for Screening Potentially Carcinogenic DNA Adducts by Trapping DNA Repair Intermediates, Nucleic Acids Res., 48, e13, 10.1093/nar/gkz1077 Kang, 2018, Electrophoretic Cytopathology Resolves ERBB2 Forms with Single-Cell Resolution, NPJ Precis. Oncol., 2, 10, 10.1038/s41698-018-0052-3 Kang, 2016, Single Cell-Resolution Western Blotting, Nat. Protoc., 11, 1508, 10.1038/nprot.2016.089 Mcquin, 2018, CellProfiler 3.0: Next-Generation Image Processing for Biology, PLoS Biol., 16, e2005970, 10.1371/journal.pbio.2005970 Berg, 2019, Ilastik: Interactive Machine Learning for (Bio)Image Analysis, Nat. Methods, 16, 1226, 10.1038/s41592-019-0582-9 Perkel, 2019, Starfish Enterprise: RNA Goes Spatial, Nature, 572, 549, 10.1038/d41586-019-02477-9 Yamauchi, 2017, Sub-Cellular Western Blotting of Single Cells, Microsyst. Nanoeng., 3, 16079, 10.1038/micronano.2016.79 Jackson, 2013, Clinical Significance of HER-2 Splice Variants in Breast Cancer Progression and Drug Resistance, Int. J. Cell Biol., 2013, 1, 10.1155/2013/973584 Giddings, 1991, 97 Glantz, 2005 Cai, 2006, Stochastic Protein Expression in Individual Cells at the Single Molecule Level, Nature, 440, 358, 10.1038/nature04599 Bonett, 2006, Confidence Interval for a Coefficient of Quartile Variation, Comput. Stat. Data Anal., 50, 2953, 10.1016/j.csda.2005.05.007 Wheelock, 2006, Effects of Post-Electrophoretic Analysis on Variance in Gel-Based Proteomics, Expert Rev. Proteomics, 3, 129, 10.1586/14789450.3.1.129 Begley, 2012, Drug Development: Raise Standards for Preclinical Cancer Research, Nature, 483, 531, 10.1038/483531a Peng, 2011, Reproducible Research in Computational Science, Science (80-)., 334, 1226, 10.1126/science.1213847 Ju, 2015, Development of a Robust Classifier for Quality Control of Reverse-Phase Protein Arrays, Bioinformatics, 31, 912, 10.1093/bioinformatics/btu736 Wheelock, 2005, Software-Induced Variance in Two-Dimensional Gel Electrophoresis Image Analysis, Electrophoresis, 26, 4508, 10.1002/elps.200500253 Shannon Neeley, 2012, Surface Adjustment of Reverse Phase Protein Arrays Using Positive Control Spots, Cancer Inform., 11, 77 Zhu, 2006, ProCAT: A Data Analysis Approach for Protein Microarrays, Genome Biol., 7, R110, 10.1186/gb-2006-7-11-r110 Duncombe, 2015, Hydrogel Pore-Size Modulation for Enhanced Single-Cell Western Blotting, Adv. Mater., 28, 327, 10.1002/adma.201503939 Berth, 2008, The State of the Art in the Analysis of Two-Dimensional Gel Electrophoresis Images, Appl. Microbiol. Biotechnol., 79, 329, 10.1007/s00253-008-1452-z Goez, 2018, Preprocessing of 2-Dimensional Gel Electrophoresis Images Applied to Proteomic Analysis: A Review, Genom. Proteom. Bioinforma, 16, 63, 10.1016/j.gpb.2017.10.001 Tsakanikas, 2007, Effective Denoising of 2D Gel Proteomics Images Using Contourlets, 269 Kim, 2018, Microparticle Delivery of Protein Markers for Single-Cell Western Blotting from Microwells, Small, 14, e1802865, 10.1002/smll.201802865 Vohradský, 1993, Quantitative Analysis of Gel Electrophoretograms by Image Analysis and Least Squares Modeling, Electrophoresis, 14, 601, 10.1002/elps.1150140195 Mitra, 2009, An Oncogenic Isoform of HER2 Associated with Locally Disseminated Breast Cancer and Trastuzumab Resistance, Mol. Cancer Ther., 8, 2152, 10.1158/1535-7163.MCT-09-0295 Solakidi, 2005, Estrogen Receptors Alpha and Beta (ERalpha and ERbeta) and Androgen Receptor (AR) in Human Sperm: Localization of ERbeta and AR in Mitochondria of the Midpiece, Hum. Reprod., 20, 3481, 10.1093/humrep/dei267 Okoro, 2012, Splicing up Mdm2 for Cancer Proteome Diversity, Genes Cancer, 3, 311, 10.1177/1947601912455323 Rajan, 2009, Alternative Splicing and Biological Heterogeneity in Prostate Cancer, Nat. Rev. Urol., 6, 454, 10.1038/nrurol.2009.125 Kim, 2017, High-Selectivity Cytology via Lab-on-a-Disc Western Blotting of Individual Cells, Lab Chip, 17, 855, 10.1039/C6LC01333C Caballero, 2002, Parabolic-Lorentzian Modified Gaussian Model for Describing and Deconvolving Chromatographic Peaks, J. Chromatogr. A, 954, 59, 10.1016/S0021-9673(02)00194-2 Shadle, 1997, Quantitative Analysis of Electrophoresis Data: Novel Curve Fitting Methodology and Its Application to the Determination of a Protein-DNA Binding Constant, Nucleic Acids Res., 25, 850, 10.1093/nar/25.4.850 Sinkala, 2017, Profiling Protein Expression in Circulating Tumour Cells Using Microfluidic Western Blotting, Nat. Commun., 8, 14622, 10.1038/ncomms14622 Orengo, 1997, CATH—A Hierarchic Classification of Protein Domain Structures, Structure, 5, 1093, 10.1016/S0969-2126(97)00260-8