Schema for Combined Exo-seq TSS - Combined Transcription Start Sites Identified by Exo-seq

Database: dm6 Primary Table: tss_exoseq_CAGE_Peaks Row Count: 7,976 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	59236	`int(10) unsigned`	range
`chromEnd`	59264	`int(10) unsigned`	range
`name`	2_1	`varchar(255)`	values
`score`	0	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	59236	`int(10) unsigned`	range
`thickEnd`	59264	`int(10) unsigned`	range
`reserved`	255	`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	59236	59264	2_1	-	59236	59264	255
585	chr2L	72598	72638	0_0	+	72598	72638	16711680
585	chr2L	94734	94749	2_1	+	94734	94749	255
585	chr2L	102380	102460	0_0	+	102380	102460	16711680
585	chr2L	107748	107797	0_0	+	107748	107797	16711680
585	chr2L	108130	108188	0_0	+	108130	108188	16711680
585	chr2L	108589	108765	0_0	+	108589	108765	16711680
585	chr2L	112911	113142	2_0	+	112911	113142	65280
585	chr2L	120474	120497	0_1	-	120474	120497	16766720
585	chr2L	123178	123361	2_1	-	123178	123361	255

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

Combined Exo-seq TSS (tss_exoseq_Combined) Track Description


	Description These tracks show the normalized density of the combined Exo-seq reads from D. melanogaster collected at different Zeitgeber Times (ZT) and temperatures. The Exo-seq datasets were obtained from the NCBI Sequence Read Archive database under the accession number SRP045351. Methods Each dataset was mapped to the D. melanogaster release 6 assembly using bwa with default parameters. 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 Afik S, Bartok O, Artyomov MN, Shishkin AA, Kadri S, Hanan M, Zhu X, Garber M, Kadener S. Defining the 5′ and 3′ landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq. Nucleic Acids Res. 2017 Jun 20;45(11):e95. 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