Single Molecule Sequencing: Epigenomics

Instructors: Theodore M. Nelson, Christopher E. Mason
Lecture Summary: Epigenomics provides a key avenue for understanding biological aging and difference. There are many diverse biological phenotypes which have been directly tied to CPG islets and DNA epigenomic modifications. Additionally, this lecture includes a discussion of HW2.
Course Summary: Sequencing-based research has become the dominant investigative practice within the biological sciences. Single-molecule sequencing: training, methods, and applications, responds to this development by providing a hands-on and in-depth introduction to sequencing for students, from Sanger to third-generation technologies. Utilizing an alternating lecture-lab schedule, students are introduced to fundamental basic principles of DNA & RNA science, progressing to cutting-edge library preparation and sequencing analysis techniques with Illumina and Nanopore technologies. Students will have the opportunity to perform direct-RNA sequencing samples on research samples, and experience first-hand the ethical implications of this data. Relevant concepts in biology and computer science will be addressed.
GitHub Link: github.com/The...
Relevant Papers:
Desai, P., Mencia-Trinchant, N., Savenkov, O. et al. Somatic mutations precede acute myeloid leukemia years before diagnosis. Nat Med 24, 1015-1023 (2018). doi.org/10.103...
Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, Heine-Suñer D, Cigudosa JC, Urioste M, Benitez J, Boix-Chornet M, Sanchez-Aguilera A, Ling C, Carlsson E, Poulsen P, Vaag A, Stephan Z, Spector TD, Wu YZ, Plass C, Esteller M. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10604-9. doi: doi.org/10.107... . Epub 2005 Jul 11. PMID: 16009939; PMCID: PMC1174919.
Horvath, S. DNA methylation age of human tissues and cell types. Genome Biol 14, 3156 (2013). doi.org/10.118...
Weidner, C.I., Lin, Q., Koch, C.M. et al. Aging of blood can be tracked by DNA methylation changes at just three CpG sites. Genome Biol 15, R24 (2014). doi.org/10.118...
Gary Dixon et al. ,QSER1 protects DNA methylation valleys from de novo methylation.Science372,eabd0875(2021).DOI: doi.org/10.112...
Zook, J., Catoe, D., McDaniel, J. et al. Extensive sequencing of seven human genomes to characterize benchmark reference materials. Sci Data 3, 160025 (2016). doi.org/10.103...
Foox, J., Nordlund, J., Lalancette, C. et al. The SEQC2 epigenomics quality control (EpiQC) study. Genome Biol 22, 332 (2021). doi.org/10.118...
Amanda Raine, Erika Manlig, Per Wahlberg, Ann-Christine Syvänen, Jessica Nordlund, SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing, Nucleic Acids Research, Volume 45, Issue 6, 7 April 2017, Page e36, doi.org/10.109...
Garrett-Bakelman FE, Darshi M, Green SJ, Gur RC, Lin L, Macias BR, McKenna MJ, Meydan C, Mishra T, Nasrini J, Piening BD, Rizzardi LF, Sharma K, Siamwala JH, Taylor L, Vitaterna MH, Afkarian M, Afshinnekoo E, Ahadi S, Ambati A, Arya M, Bezdan D, Callahan CM, Chen S, Choi AMK, Chlipala GE, Contrepois K, Covington M, Crucian BE, De Vivo I, Dinges DF, Ebert DJ, Feinberg JI, Gandara JA, George KA, Goutsias J, Grills GS, Hargens AR, Heer M, Hillary RP, Hoofnagle AN, Hook VYH, Jenkinson G, Jiang P, Keshavarzian A, Laurie SS, Lee-McMullen B, Lumpkins SB, MacKay M, Maienschein-Cline MG, Melnick AM, Moore TM, Nakahira K, Patel HH, Pietrzyk R, Rao V, Saito R, Salins DN, Schilling JM, Sears DD, Sheridan CK, Stenger MB, Tryggvadottir R, Urban AE, Vaisar T, Van Espen B, Zhang J, Ziegler MG, Zwart SR, Charles JB, Kundrot CE, Scott GBI, Bailey SM, Basner M, Feinberg AP, Lee SMC, Mason CE, Mignot E, Rana BK, Smith SM, Snyder MP, Turek FW. The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science. 2019 Apr 12;364(6436):eaau8650. doi: doi.org/10.112... . PMID: 30975860; PMCID: PMC7580864.
Course website: physiology.med...
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