Single Molecule Sequencing: Spatial Transcriptomics

Instructors: Robert E. Schwartz
Lecture Summary: In this lecture, Professor Robert E. Schwartz, MD-PhD, Associate Professor of Medicine at Weill Cornell, describes recent advances in spatial-omics technologies and tissue-specific considerations. These include the pros and cons of various spatial and subspatial profiling technologies, in terms of coverage, number of detected genes, and resolution. He provides a broad overview of current efforts to classify phenotypically normal tissue, before proceeding to highlights from two specific clinically relevant case studies: Alagille syndrome and COVID-19.
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.
Relevant Papers:
Gupta V, Gupta I, Park J, Bram Y, Schwartz RE. Hedgehog Signaling Demarcates a Niche of Fibrogenic Peribiliary Mesenchymal Cells. Gastroenterology. 2020 Aug;159(2):624-638.e9. doi: doi.org/10.105.... Epub 2020 Apr 11. PMID: 32289375; PMCID: PMC8204800.
Park J, Foox J, Hether T, Danko D, Warren S, Kim Y, Reeves J, Butler DJ, Mozsary C, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Bram Y, Chandar V, Geiger H, Craney A, Velu P, Melnick AM, Hajirasouliha I, Beheshti A, Taylor D, Saravia-Butler A, Singh U, Wurtele ES, Schisler J, Fennessey S, Corvelo A, Zody MC, Germer S, Salvatore S, Levy S, Wu S, Tatonetti N, Shapira S, Salvatore M, Loda M, Westblade LF, Cushing M, Rennert H, Kriegel AJ, Elemento O, Imielinski M, Borczuk AC, Meydan C, Schwartz RE, Mason CE. Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps. bioRxiv [Preprint]. 2021 Mar 9:2021.03.08.434433. doi: doi.org/10.110... PMID: 33758858; PMCID: PMC7987017.
Huppert SS, Schwartz RE. Multiple Facets of Cellular Homeostasis and Regeneration of the Mammalian Liver. Annu Rev Physiol. 2023 Feb 10;85:469-493. doi: doi.org/10.114... Epub 2022 Oct 21. PMID: 36270290; PMCID: PMC9918695.
Course website: physiology.med...
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