CometChip Data Analysis – Running the Guicometanalyzer in Debug mode
Simran Kaushal, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States and Department of Environmental Health, Harvard School of Public Health, Boston, MA, United States
kaushal@mit.eduPROTOCOL TYPE:
Protocol Document
SYNOPSIS:
Any time CometChip is performed on a new cell type, it is important to confirm that you are using appropriate parameters for analyzing your data set. This can be done by choosing a representative well image and analyzing it in a special “debug” mode in the Guicometanalyzer, as illustrated in this protocol.
Xiong A, Prakash P, Gao X, Chew M, Tay IJJ, Woodrow CJ, Engelward BP, Han J, Preiser PR. K13-Mediated Reduced Susceptibility to Artemisinin in Plasmodium falciparum Is Overlaid on a Trait of Enhanced DNA Damage Repair. Cell Rep. 2020 Aug 4;32(5):107996. doi: 10.1016/j.celrep.2020.107996. PMID: 32755588; PMCID: PMC7408483.
Tay IJ, Park JJH, Price AL, Engelward BP, Floyd SR. HTS-Compatible CometChip Enables Genetic Screening for Modulators of Apoptosis and DNA Double-Strand Break Repair. SLAS Discov. 2020 Sep;25(8):906-922. doi: 10.1177/2472555220918367. Epub 2020 May 26. PMID: 32452708.
Ngo LP, Owiti NA, Swartz C, Winters J, Su Y, Ge J, Xiong A, Han J, Recio L, Samson LD, Engelward BP. Sensitive CometChip assay for screening potentially carcinogenic DNA adducts by trapping DNA repair intermediates. Nucleic Acids Res. 2020 Feb 20;48(3):e13. doi: 10.1093/nar/gkz1077. PMID: 31822921; PMCID: PMC7026589.
Chao C, Ngo Le P, Engelward BP. SpheroidChip: Patterned Agarose Microwell Compartments Harboring HepG2 Spheroids are Compatible with Genotoxicity Testing. ACS Biomater Sci Eng. 2020 Apr 13;6(4):2427-2439. doi: 10.1021/acsbiomaterials.9b01951. Epub 2020 Mar 2. PMID: 33145399; PMCID: PMC7603797.
Parrish MC, Chaim IA, Nagel ZD, Tannenbaum SR, Samson LD, Engelward BP. Nitric oxide induced S-nitrosation causes base excision repair imbalance. DNA Repair (Amst). 2018 Aug;68:25-33. doi: 10.1016/j.dnarep.2018.04.008. Epub 2018 May 5. PMID: 29929044; PMCID: PMC6436541.
Sykora P, Witt KL, Revanna P, Smith-Roe SL, Dismukes J, Lloyd DG, Engelward BP, Sobol RW. Next generation high throughput DNA damage detection platform for genotoxic compound screening. Sci Rep. 2018 Feb 9;8(1):2771. doi: 10.1038/s41598-018-20995-w. PMID: 29426857; PMCID: PMC5807538.
Townsend TA, Parrish MC, Engelward BP, Manjanatha MG. The development and validation of EpiComet-Chip, a modified high-throughput comet assay for the assessment of DNA methylation status. Environ Mol Mutagen. 2017 Aug;58(7):508-521. doi: 10.1002/em.22101. Epub 2017 Jul 29. PMID: 28755435; PMCID: PMC5839338.
Ge J, Chow DN, Fessler JL, Weingeist DM, Wood DK, Engelward BP. Micropatterned comet assay enables high throughput and sensitive DNA damage quantification. Mutagenesis. 2015 Jan;30(1):11-9. doi: 10.1093/mutage/geu063. PMID: 25527723; PMCID: PMC4272061.
Ge J, Prasongtanakij S, Wood DK, Weingeist DM, Fessler J, Navasummrit P, Ruchirawat M, Engelward BP. CometChip: a high-throughput 96-well platform for measuring DNA damage in microarrayed human cells. J Vis Exp. 2014 Oct 18;(92):e50607. doi: 10.3791/50607. PMID: 25350601; PMCID: PMC4407627.
Watson C, Ge J, Cohen J, Pyrgiotakis G, Engelward BP, Demokritou P. High-throughput screening platform for engineered nanoparticle-mediated genotoxicity using CometChip technology. ACS Nano. 2014 Mar 25;8(3):2118-33. doi: 10.1021/nn404871p. Epub 2014 Mar 11. PMID: 24617523;
PMCID: PMC3971959.
Ge J, Wood DK, Weingeist DM, Prasongtanakij S, Navasumrit P, Ruchirawat M, Engelward BP. Standard fluorescent imaging of live cells is highly genotoxic. Cytometry A. 2013 Jun;83(6):552-60. doi: 10.1002/cyto.a.22291. Epub 2013 May 6. PMID: 23650257; PMCID: PMC3677558.
Weingeist DM, Ge J, Wood DK, Mutamba JT, Huang Q, Rowland EA, Yaffe MB, Floyd S, Engelward BP. Single-cell microarray enables high-throughput evaluation of DNA double-strand breaks and DNA repair inhibitors. Cell Cycle. 2013 Mar 15;12(6):907-15. doi: 10.4161/cc.23880. Epub 2013 Feb 19. PMID: 23422001; PMCID: PMC3637349.
Wood DK, Weingeist DM, Bhatia SN, Engelward BP. Single cell trapping and DNA damage analysis using microwell arrays. Proc Natl Acad Sci U S A. 2010 Jun 1;107(22):10008-13. doi: 10.1073/pnas.1004056107. Epub 2010 May 13. PMID: 20534572; PMCID: PMC2890454.
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