TSRchitect RAMPAGE Embryos TSS Track Settings

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TSRchitect RAMPAGE Embryos Transcription Start Sites (All Updated Transcriptome Tracks)

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	hide Configure	Embryos, 1 hr	RAMPAGE Peaks for 1 hr Embryo	Schema
	hide Configure	Embryos, 2 hr	RAMPAGE Peaks for 2 hr Embryo	Schema
	hide Configure	Embryos, 3 hr	RAMPAGE Peaks for 3 hr Embryo	Schema
	hide Configure	Embryos, 4 hr	RAMPAGE Peaks for 4 hr Embryo	Schema
	hide Configure	Embryos, 5 hr	RAMPAGE Peaks for 5 hr Embryo	Schema
	hide Configure	Embryos, 6 hr	RAMPAGE Peaks for 6 hr Embryo	Schema
	hide Configure	Embryos, 7 hr	RAMPAGE Peaks for 7 hr Embryo	Schema
	hide Configure	Embryos, 8 hr	RAMPAGE Peaks for 8 hr Embryo	Schema
	hide Configure	Embryos, 9 hr	RAMPAGE Peaks for 9 hr Embryo	Schema
	hide Configure	Embryos, 10 hr	RAMPAGE Peaks for 10 hr Embryo	Schema
	hide Configure	Embryos, 11 hr	RAMPAGE Peaks for 11 hr Embryo	Schema
	hide Configure	Embryos, 12 hr	RAMPAGE Peaks for 12 hr Embryo	Schema
	hide Configure	Embryos, 13 hr	RAMPAGE Peaks for 13 hr Embryo	Schema
	hide Configure	Embryos, 14 hr	RAMPAGE Peaks for 14 hr Embryo	Schema
	hide Configure	Embryos, 15 hr	RAMPAGE Peaks for 15 hr Embryo	Schema
	hide Configure	Embryos, 16 hr	RAMPAGE Peaks for 16 hr Embryo	Schema
	hide Configure	Embryos, 17 hr	RAMPAGE Peaks for 17 hr Embryo	Schema
	hide Configure	Embryos, 18 hr	RAMPAGE Peaks for 18 hr Embryo	Schema
	hide Configure	Embryos, 19 hr	RAMPAGE Peaks for 19 hr Embryo	Schema
	hide Configure	Embryos, 20 hr	RAMPAGE Peaks for 20 hr Embryo	Schema
	hide Configure	Embryos, 21 hr	RAMPAGE Peaks for 21 hr Embryo	Schema
	hide Configure	Embryos, 22 hr	RAMPAGE Peaks for 22 hr Embryo	Schema
	hide Configure	Embryos, 23 hr	RAMPAGE Peaks for 23 hr Embryo	Schema

Description

This track shows the locations of putative Transcription Start Sites (TSS) in the D. melanogaster genome based on the analysis of RAMPAGE data from different embryonic stages in one-hour intervals.

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.

References

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.