Uploaded November 2022 | Updated September 2026, 1 week ago
Sebastian Pineda, MIT
Tutorial on transcriptomic assays - TRAP and snRNA-seq sequencing with Sebastian Pineda
High-throughput sequencing assays have become ubiquitous and indispensable tools in molecular neurobiology. They provide a means to investigate gene expression, dissect gene interactions and pathways, and examine how these change in model systems and disease. Recent developments in transcriptomics have yielded methods that allow us to survey gene expression with cell-type specificity at varying degrees of resolution. In this tutorial, I will give a brief overview of two common cell-type specific transcriptomic assays: TRAP (translating ribosome affinity purification) and snRNA-seq (single-nucleus RNA) sequencing. I will introduce the types of data that these assays generate and discuss the advantages and use cases of each. The bulk of the tutorial will focus on a typical data preprocessing and analysis workflow covering the topics dimensionality reduction, count normalization, clustering, and cell type annotation, as well as key downstream analysis concepts such as differential gene expression and pathway enrichment. Lastly, I will showcase recently developed tools and software packages that facilitate more sophisticated methods such as batch correction, data imputation, and network construction to simplify and enhance large-scale transcriptomics data analysis.
Sebastian's website: https://heiman.mit.edu/team/pineda-sebastian/
Sebastian Pineda, MIT
Tutorial on transcriptomic assays - TRAP and snRNA-seq sequencing with Sebastian Pineda
High-throughput sequencing assays have become ubiquitous and indispensable tools in molecular neurobiology. They provide a means to investigate gene expression, dissect gene interactions and pathways, and examine how these change in model systems and disease. Recent developments in transcriptomics have yielded methods that allow us to survey gene expression with cell-type specificity at varying degrees of resolution. In this tutorial, I will give a brief overview of two common cell-type specific transcriptomic assays: TRAP (translating ribosome affinity purification) and snRNA-seq (single-nucleus RNA) sequencing. I will introduce the types of data that these assays generate and discuss the advantages and use cases of each. The bulk of the tutorial will focus on a typical data preprocessing and analysis workflow covering the topics dimensionality reduction, count normalization, clustering, and cell type annotation, as well as key downstream analysis concepts such as differential gene expression and pathway enrichment. Lastly, I will showcase recently developed tools and software packages that facilitate more sophisticated methods such as batch correction, data imputation, and network construction to simplify and enhance large-scale transcriptomics data analysis.
Sebastian's website: https://heiman.mit.edu/team/pineda-sebastian/
