Meg Laakso

Module TSS3: CAGE, RAMPAGE, and RNA Pol II X-ChIP-Seq

August 15, 2020January 15, 2023

This module uses the placement of the Initiator (Inr) motif, TSS annotations produced by the Celniker group at modENCODE, and experimental data such as CAGE, RAMPAGE, and RNA Polymerase II X-ChIP-Seq data to characterize the promoter for the Antp gene in D. melanogaster.

Module TSS2: Using Sequence Alignment to Identify a TSS

August 15, 2020January 15, 2023

This module illustrates how pairwise (blastn) and multiple sequence alignments can be used in conjunction with RNA-Seq data and the Short Match functionality of the UCSC Genome Browser to facilitate the TSS annotation of the Antp gene in D. eugracilis.

Module TSS1: Transcription Start Sites Introduction

August 15, 2020January 15, 2023

This module describes how Celniker TSS annotations, DNase I hypersensitive sites, and the 9-state chromatin models can be used in the classification of promoter shape for the Antp gene.

TSS Module Primer: Review of Transcription, Promoter Structure, and Chromatin Packaging

August 15, 2020January 15, 2023

This primer includes some biological concepts that may be helpful to review prior to working with the four TSS Modules, including: a brief review of gene transcription, mRNA processing, promoter structure, and chromatin.

Glossary for Understanding Eukaryotic Genes

August 15, 2020January 14, 2023

This glossary defines the key terms that are used in the Understanding Eukaryotic Genes modules.

Module 4. Removal of introns from pre-mRNA by splicing

August 15, 2020January 15, 2023

This module uses mRNA data to identify splice sites. After completing this module students will be able to identify intron-exon boundaries using canonical splice donor and acceptor sequences and determine which are best supported by RNA-Seq and TopHat splice junction predictions.