
Week	Tue Lecture	Tue/Thur Labs	Thur Lecture	Sun HW Due
5 (2/24)	[On Module 1 page]	[On Module 1 page]	Motif finding Slides Lecture videos: Transcription Regulation Expectation Maximization Gibbs Sampler General Practices Other videos: Transcription regulation Post-transcriptional regulation Gibbs sampling Expectation Maximization Motif discovery
6 (3/2)	ChIP-seq and integration with expression Slides Lecture Videos ChIP-seq MACS and QC TF Interactions TF Target Genes Other Videos ChIP-seq MACS Cistrome AP Cistrome DB	Stat115 Lab 6 https://github.com/stat115/Lab_2020/tree/master/Lab06	Epigenetics, DNA methylation Slides Lecture Videos: Epigenetics DNA Methylation DNA Methylation Function Nucleosome Position Other Videos Basic intro1 Basic intro2 CpG islands and DNA methylation DNA methylation and cancer DNA methylation analyses	HW3 (Classification, scRNA-seq)
7 (3/9)	Histone modifications, Chromatin accessibility Slides Lecture videos Histone modifications Histone marks on enhancers Histone marks on genes DNase-seq ATAC-seq Other videos: Histone modifications DNase-seq ATAC-seq	Macs2, BedTools, Cistrome Zoom Video	Hidden Markov Model Slides Lecture videos 1 2 3 4 Other videos: HMM Intro HMM Applications Forward-backward algorithm Viterbi algorithm
8 (3/16)	Spring Recess		Spring Recess
9 (3/23)	Long range chromatin interactions Slides Lecture videos HiC Intro TADs Compartments Regulatory Network Other videos HiC (start at 4:30) Chromosome organization Loop extrusion model Enhancer Target Gene Prediction	Lab8 Material Lab8 Recording	scRNA-seq and scATAC-seq integration Slides Lecture Videos Intro to scATAC-seq Preprocess and QC scATAC-seq Analysis of scATAC-seq Integrate scATAC-seq and scRNA-seq Other videos: LISA	HW4 (ChIP-seq and expression integration)
10 (3/30)	Module II Review Slides Videos: Module II Review Practice Questions GWAS Intro GWAS Issues and eQTL	scATAC-seq, SCREEN	[On Module 3 Page]