Schema for Combined RAMPAGE TSS - Combined RAMPAGE Transcription Start Sites

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Schema for Combined RAMPAGE TSS - Combined RAMPAGE Transcription Start Sites

Database: DpseGB3 Primary Table: RAMPAGE2_Combined_plus Row Count: 1 Data last updated: 2022-10-20

field	example	SQL type	info
`fileName`	/gbdb/DpseGB3/bbi/RAMPAGE2/...	`varchar(255)`	values

This table points to a file in BigWig format.

Sample Rows

fileName
/gbdb/DpseGB3/bbi/RAMPAGE2/GSE89300_Dpse_Combined_plus.bw

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.