TEACHING MATERIALS: Guest Lectures

Designing RNA-Seq experiments:

Eric Antoniou, Ph.D.

Designing RNA-Seq experiments

Illumina library preparation and sequencing technology:

Michael Ronan

Illumina TruSeq RNA libraries: Part I–Start prep

Michael Ronan

Illumina TruSeq RNA libraries: Part II–Continue prep

Analyzing RNA-Seq data:

Elena Ghiban

Processing raw sequencing reads

Nicolas Robine, Ph.D.

Understanding NGS sequencing files

Nicolas Robine, Ph.D.

RNA-Seq analysis pipeline: TUXEDO protocol

Molly Hammell, Ph.D.

RNA-Seq for differential gene expression: the tuxedo suite

Stephen Turner, Ph.D.

RNA-Seq experimental design, quality control and analysis of differential gene expression - Part I

Stephen Turner, Ph.D.

RNA-Seq experimental design, quality control and analysis of differential gene expression - Part II

Harold Pimentel, Ph.D.

Part I: Aligning and visualizing RNA-Seq data with TopHat and IGV

Harold Pimentel, Ph.D.

Part II: Quantifying transcripts with CuffLinks

Harold Pimentel, Ph.D.

Part III: Determining differential gene expression; p- and q-values

Harold Pimentel, Ph.D.

Part IV: Alternative RNA-Seq data analysis pipelines; Sailfish and Kallisto

Validation of candidate genes and downstream analyses with RNA-Seq data:

Sarah Diermeier, Ph.D.

Validating RNA-Seq Data by qRT-PCR

Thomas Lombardi, D.P.S.

Biological networks, Cytoscape and BiNGO

Other lectures:

Michael Schatz, Ph.D.

Dickens to DNA: Introduction to de novo sequence assembly

Tom Gingeras, Ph.D.

The ENCODE project

Charla Lambert, Ph.D.

Advanced data analysis: Command line usage

Andy Larrea, Ph.D.

Applications in SMRT sequencing: Using long reads to understand the transcriptome

Vasily Vagin, Ph.D.

Demo: Small RNA isolation from total RNA

Rob Martienssen, Ph.D.

Genome complexity and epigenetic regulation

Ross Nehm, Ph.D.

Best practices for STEM curriculum development

Brent Buckner, Ph.D.

Initiating, developing and maintaining NGS skills while working with undergraduate students–a case study