Schema for Combined MachiBase TSS - Combined MachiBase Transcription Start Sites

Database: dm6 Primary Table: tss_MachiBase_Peaks Row Count: 7,480 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	108131	`int(10) unsigned`	range
`chromEnd`	108142	`int(10) unsigned`	range
`name`	0_0	`varchar(255)`	values
`score`	0	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	108131	`int(10) unsigned`	range
`thickEnd`	108142	`int(10) unsigned`	range
`reserved`	16711680	`int(10) unsigned`	range

This table points to a file in BigWig format.

Sample Rows

bin	chrom	chromStart	chromEnd	name	strand	thickStart	thickEnd	reserved
585	chr2L	108131	108142	0_0	+	108131	108142	16711680
585	chr2L	112921	113095	0_1	+	112921	113095	16766720
585	chr2L	121746	121751	0_0	-	121746	121751	16711680
585	chr2L	123258	123432	1_1	-	123258	123432	11177813
585	chr2L	123881	124029	3_1	-	123881	124029	255
585	chr2L	126209	126217	0_0	-	126209	126217	16711680
585	chr2L	128966	128987	0_0	-	128966	128987	16711680
586	chr2L	132046	132120	0_1	+	132046	132120	16766720
586	chr2L	142525	142594	2_0	-	142525	142594	5614080
586	chr2L	155304	155680	1_0	+	155304	155680	11162880

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

Combined MachiBase TSS (tss_MachiBase_Combined) Track Description


	Description These tracks show the normalized density of SAGE reads from different developmental stages of D. melanogaster. The datasets were produced by MachiBase and were obtained from the NCBI BioProject database under the accession number PRJNA79391. Methods Each dataset was mapped to the D. melanogaster release 6 assembly using bwa and the alignment results were analyzed by CAGEr. Consensus promoters across all the samples were produced by the consensusClusters function in CAGEr with the following parameters: `tpmThreshold = 5, qLow = 0.1, qUp = 0.9, maxDist = 100` Credits Ahsan B, Saito TL, Hashimoto S, Muramatsu K, Tsuda M, Sasaki A, Matsushima K, Aigaki T, Morishita S. MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database. Nucleic Acids Res. 2009 Jan;37(Database issue):D49-53. Haberle V, Forrest AR, Hayashizaki Y, Carninci P, Lenhard B. CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Nucleic Acids Res. 2015 Apr 30;43(8):e51.

Description