This track shows the locations of putative Transcription Start Sites (TSS) in the
D. melanogaster genome based on the analysis of RAMPAGE results from multiple embryonic stages of D. melanogaster.
The embryos RAMPAGE datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession numbers GSE36212 and GSE89299. The RAMPAGE reads were mapped against the D. melanogaster (dm6) assembly using STAR. The putative promoter regions were identified by TSRchitect and icetea.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21.
Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR.
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.
Genome Res. 2013 Jan;23(1):169-80.