Bio-Trac: Single Cell RNA-Seq

4-Day Training Workshop

This in-depth lecture and hands-on laboratory workshop (wet lab & in silica) is ideal for those research and bench scientists who are interested in a comprehensive introduction to single cell RNA-Seq. The core of this workshop is composed of highlighting key aspects of NSG and RNA-seq methodologies, with subsequent introduction into the modern armamentarium of tools to conduct these experiments. Further emphasis will be placed on such important aspects as sample preparation, quality control validation and enrichment as well as extensive use of different single cell RNA-Seq data analysis tools (Seurat, Monocle, Pseudo-time Analysis, Clustering Analysis in-depth: t-SNE and Principal Component Analysis).

Overview of Lecture:

Lectures Topics

• Introduction to Next Generation Sequencing (NGS) and RNA-seq
• Single cell RNA-seq: Principles and Methods
• Sample Preparation and Validation for Single Cell Sequencing
• Drop-seq, High Throughput Single Cell RNA-seq
• 10x Genomics: Chromium Controller Single Cell 3 Work Flow
• Illumina-Biorad’s ddSeq: Data Analysis with BaseSpace; SureCell RNA Single-Cell app
• Comparison of Single Cell RNA-Seq Platforms: Drop-Seq, 10X Genomics, Illumina ddSeq and Fluidigm
• Pre-requisites for Single Cell RNA-seq Analysis: Linux command-line & R Review

Lecture and Hands-on In Silica laboratory:

• Single Cell RNA-seq Analysis: Analysis with Seurat; Analysis with Monocle
• Recent Development of Various seq’s: Related Single Cell RNA-seq, SPLiT-seq, Seq-Well
• Differential Gene Expression Analysis for Single Cell RNA-seq
• TSCAN: Pseudo-time Analysis
• Normalizations in Single Cell RNA-seq
• Clustering Analysis in-depth, Particularly for t-SNE and Principal Component Analysis

Wet Laboratory

• Sample Preparation and Validation for Single Cell Sequencing: Tissue Dissociation, Dead Cell Removal as well as other Contaminants, Pre-enrichment Prior to Single-cell Sequencing