Schema for TSRchitect Combined RAMPAGE TSS - TSRchitect Combined RAMPAGE Transcription Start Sites

JavaScript is disabled in your web browser

You must have JavaScript enabled in your web browser to use the Genome Browser

Schema for TSRchitect Combined RAMPAGE TSS - TSRchitect Combined RAMPAGE Transcription Start Sites

Database: DanaCAF1 Primary Table: RAMPAGE2_star_Combined_plus Row Count: 1 Data last updated: 2022-10-20

field	example	SQL type	info
`fileName`	/gbdb/DanaCAF1/bbi/RAMPAGE2...	`varchar(255)`	values

This table points to a file in BigWig format.

Sample Rows

fileName
/gbdb/DanaCAF1/bbi/RAMPAGE2_star/GSE89298_rampage_combined.plus.bw

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

TSRchitect Combined RAMPAGE TSS (tss_RAMPAGE2_star_Combined) Track Description


	Description This track shows the locations of putative Transcription Start Sites (TSS) in the D. ananassae genome based on the analysis of RAMPAGE results from multiple developmental stages of D. ananassae embryos. The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number GSE89298. The RAMPAGE reads were mapped against the D. ananassae (DanaCAF1) 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 PJ, Gingeras TR. Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. Elife. 2017 Dec 20;6.