TSS Annotation

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

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

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

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.

Annotation of Transcription Start Sites in Drosophila

This walkthrough illustrates the GEP protocol for the comparative annotation of transcription start sites (TSS) in D. biarmipes. The walkthrough also includes a sample GEP TSS Report for the TSS annotation of onecut.

Searching for Transcription Start Sites in Drosophila

This PowerPoint presentation describes the recommended annotation strategy for identifying transcription start sites in Drosophila. The presentation provides an overview of the promoter architecture in D. melanogaster and describes the types of evidence that can be used to support the transcription start sites annotations.