Schema for Combined RAMPAGE TSS - Combined RAMPAGE Transcription Start Sites

Database: DereCAF1 Primary Table: tss_RAMPAGE2_Peaks Row Count: 22,632 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_1029	`varchar(255)`	values
`chromStart`	870	`int(10) unsigned`	range
`chromEnd`	883	`int(10) unsigned`	range
`name`	RAMPAGEpeak_018368	`varchar(255)`	values
`score`	20	`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	scaffold_1029	870	883	RAMPAGEpeak_018368	20	+
585	scaffold_1031	899	908	RAMPAGEpeak_015754	25	-
585	scaffold_1121	879	892	RAMPAGEpeak_018384	18	-
585	scaffold_1180	970	996	RAMPAGEpeak_007504	185	+
585	scaffold_1182	1177	1187	RAMPAGEpeak_007503	987	+
585	scaffold_1194	1280	1281	RAMPAGEpeak_007515	18	-
585	scaffold_1213	786	821	RAMPAGEpeak_018267	12365	+
585	scaffold_1353	4004	4066	RAMPAGEpeak_018269	333	+
585	scaffold_1361	3398	3404	RAMPAGEpeak_015373	16	+
585	scaffold_1361	4360	4496	RAMPAGEpeak_015374	820	-

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. erecta 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 GSE89304. 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