Schema for Combined RAMPAGE TSS - Combined RAMPAGE Transcription Start Sites

Database: DpseGB3 Primary Table: tss_RAMPAGE2_Peaks Row Count: 26,064 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CH379058	`varchar(255)`	values
`chromStart`	608	`int(10) unsigned`	range
`chromEnd`	709	`int(10) unsigned`	range
`name`	FBgn0246716_01	`varchar(255)`	values
`score`	5467	`int(10) unsigned`	range
`strand`	-	`char(1)`	values

This table points to a file in BigWig format.

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand
585	CH379058	608	709	FBgn0246716_01	5467	-
585	CH379058	58646	58722	FBgn0081609_01	536	+
585	CH379058	58646	58722	FBgn0081612_01	536	+
585	CH379058	68385	68615	FBgn0081611_01	21418	+
585	CH379058	71107	71171	FBgn0079267_01	7754	-
585	CH379058	75471	75484	FBgn0076373_04	70	-
585	CH379058	75847	75856	FBgn0076373_03	60	-
585	CH379058	115917	116192	FBgn0076373_02	8764	-
585	CH379058	116407	116430	RAMPAGEpeak_023800	21	+
586	CH379058	138475	138504	RAMPAGEpeak_024131	64	-

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

Combined RAMPAGE TSS (tss_RAMPAGE2_Combined) Track Description


	Description This track shows the locations of putative Transcription Start Sites (TSS) in the D. pseudoobscura genome based on the analysis of RAMPAGE results from multiple stages of Drosophila embryos. The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number GSE89300. The results were lifted from the D. pseudoobscura release 2 assembly to the release 3 assembly. References Batut PJ, Gingeras TR. Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. Elife. 2017 Dec 20;6. 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.

Description