MCB 182 is a comprehensive course exploring the fundamentals of genome biology. It reviews and covers topics from gene structure and transcriptional regulation, to algorithms for analyzing genome assembly and gene ontology, to sequence alignments and DNA/protein interaction assays. The course also examines CRISPR-Cas9 for gene editing, epigenomics and chromatin analysis, applications of RNA-seq for expression analysis and visualization, physical organization of the genome through 3C/Hi-C assays, and analysis of molecular interaction networks. Lastly, the course introduces and discusses human genetic variation, from Mendelian to complex, from GWAS to epistasis, to fine-mapping causal variants, and exploring confounders in GWAS.
Overview
Syllabus
MCB 182 Lecture 1.1 - Review - Genome content.
MCB 182 Lecture 1.2 - Review - Gene structure.
MCB 182 Lecture 1.3 - Review - Transcriptional regulation.
MCB 182 Lecture 1.4 - Review - Repetitive sequences.
MCB 182 Lecture 2.1 - DNA sequencing overview.
MCB 182 Lecture 2.2 - Sanger sequencing.
MCB 182 Lecture 2.3 - Shotgun sequencing.
MCB 182 Lecture 2.4 - Illumina SBS sequencing.
MCB 182 Lecture 2.5 - PacBio, Nanopore sequencing.
MCB 182 Lecture 3.1 - Genome assembly - Overview.
MCB 182 Lecture 3.2 - Genome assembly - overlap graphs.
MCB 182 Lecture 3.3 - Genome assembly - Overlap-layout-consensus assembly.
MCB 182 Lecture 3.4 - Genome assembly - Scaffolding contigs.
MCB 182 Lecture 4.1 - Forward genetics.
MCB 182 Lecture 4.2 - Reverse genetics (siRNA, antisense oligos).
MCB 182 Lecture 4.3 - Gene editing (non CRISPR-Cas9).
MCB 182 Lecture 4.4 - CRISPR-Cas9 overview.
MCB 182 Lecture 4.5 - CRISPR-Cas9 practical considerations, applications.
MCB 182 Lecture 5.1 - CRISPR-Cas9 genome-wide screens.
MCB 182 Lecture 5.2 - Gene ontology structure.
MCB 182 Lecture 5.3 - Gene ontology annotations.
MCB 182 Lecture 5.4 - Gene ontology enrichment analysis.
MCB 182 Lecture 6.1 - Introduction to sequence alignments.
MCB 182 Lecture 6.2 - Scoring of sequence alignments.
MCB 182 Lecture 6.3 - Dotplots for sequence similarity visualization.
MCB 182 Lecture 7.1 - Overview of TF-DNA interaction assays, EMSA.
MCB 182 Lecture 7.2 - ChIP-seq.
MCB 182 Lecture 7.3 - SELEX, Protein Binding Microarrays (PBM), introduction to entropy.
MCB 182 Lecture 7.4 - Absolute entropy of DNA sequences.
MCB 182 Lecture 7.5 - Relative entropy.
MCB 182 Lecture 7.6 - Position weight matrices, sequence logos.
MCB 182 Lecture 7.7 - PWM applications in scanning the genome for TF binding, other applications.
MCB 182 Lecture 8.1 - Introduction to Epigenomics.
MCB 182 Lecture 8.2 - Histone modifications, ChIP-seq, CUT&RUN.
MCB 182 Lecture 8.3 - DNA methylation.
MCB 182 Lecture 8.4 - Chromatin accessibility (ATAC-seq).
MCB 182 Lecture 8.5 - Chromatin states.
MCB 182 Lecture 8.6 - Massively parallel reporter assays (MPRA).
MCB 182 Lecture 8.7 - ChIP-seq QC metrics.
MCB 182 Lecture 8.8 - ChIP-seq peak calling, multiple hypothesis testing.
MCB 182 Lecture 8.9 - Narrow vs broad peaks, IDR.
MCB 182 Lecture 9.1 - Introduction to RNA-seq, motivation.
MCB 182 Lecture 9.2 - Bulk RNA-seq fundamentals.
MCB 182 Lecture 9.3 - RNA-seq read mapping strategies.
MCB 182 Lecture 9.4 - RNA-seq quantification.
MCB 182 Lecture 9.5 - RNA-seq differential gene expression, batch effects.
MCB 182 Lecture 9.6 - ncRNA (miRNA, lncRNA, eRNA).
MCB 182 Lecture 9.7 - Introduction to single cell RNA sequencing (scRNA-seq).
MCB 182 Lecture 9.8 - Analysis goals of scRNA-seq.
MCB 182 Lecture 9.9 - scRNA-seq technologies.
MCB 182 Lecture 9.10 - scRNA-seq experimental design, dropout noise.
MCB 182 Lecture 9.11 - More on scRNA-seq dropout noise.
MCB 182 Lecture 9.12 - Introduction to PCA (scRNA-seq).
MCB 182 Lecture 9.13 - scRNA-seq applications (trajectory inference, visualization).
MCB 182 Lecture 10.1 - Overview of the physical organization of the genome.
MCB 182 Lecture 10.2 - DamID for mapping protein-DNA interactions.
MCB 182 Lecture 10.3 - Chromatin conformation capture (3C, 4C) assays.
MCB 182 Lecture 10.4 - Chromatin conformation capture (Hi-C) assays.
MCB 182 Lecture 10.5 - Visualization of Hi-C data, bias in the Hi-C assay.
MCB 182 Lecture 10.6 - Topologically associated domains (TADs), A/B compartments.
MCB 182 Lecture 10.7 - Chromatin looping, loop extrusion model.
MCB 182 Lecture 10.8 - Choosing 3C assay, genome assembly with Hi-C.
MCB 182 Lecture 11.1 - Introduction to molecular interaction networks.
MCB 182 Lecture 11.2 - Protein-protein interaction (PPI) networks.
MCB 182 Lecture 11.3 - Genetic interaction (GI) networks.
MCB 182 Lecture 11.4 - Regulatory interaction networks.
MCB 182 Lecture 11.5 - Co-expression networks.
MCB 182 Lecture 11.6 - Centrality measures of node importance in a gene network.
MCB 182 Lecture 11.7 - Network structural motifs and scale-free property.
MCB 182 Lecture 11.8 - Modularity of gene networks, guilt by association principles.
MCB 182 Lecture 12.1 - Introduction to human genetic variation.
MCB 182 Lecture 12.2 - Mendelian versus complex trait genetics.
MCB 182 Lecture 12.3 - GWAS for binary phenotypes.
MCB 182 Lecture 12.4 - Q-Q plots, types of genetic architectures of complex traits.
MCB 182 Lecture 12.5 - GWAS for continuous phenotypes, effect size versus statistical significance.
MCB 182 Lecture 12.6 - Confounding factors in GWAS.
MCB 182 Lecture 12.7 - More on detecting, visualizing + correcting for population structure in GWAS.
MCB 182 Lecture 12.8 - PCA for analysis of population structure in GWAS, multiple hypothesis testing.
MCB 182 Lecture 12.9 - Fine-mapping causal variants based on GWAS associations.
MCB 182 Lecture 12.10 - Epistasis, missing heritability in GWAS.
Taught by
Gerald Quon
