Paired-end analysis of transcriptional start sites

We describe an improved deep sequencing strategy, paired-end analysis of transcriptional start sites (PEAT), to globally characterize transcriptional start sites (TSSs) in a previous study [1]. It was used to explore the landscape of transcription initiation in Drosophila melanogaster embryo. Here we present a detailed protocol, with minor modifications, can be broadly applied to investigate capped transcripts in other eukaryotes, from budding yeast to rat and human cell lines.