Schema for Eye Discs ATAC-Seq - ATAC-Seq of D. simulans Eye Discs

Database: DsimGB2 Primary Table: GSE102439_eyediscs_idr Row Count: 21,462 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CM002910	`varchar(255)`	values
`chromStart`	10643	`int(10) unsigned`	range
`chromEnd`	11055	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	6.1503	`float`	range
`pValue`	41.908	`float`	range
`qValue`	39.7729	`float`	range
`peak`	198	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	CM002910	10643	11055	.	1000	.	6.1503	41.908	39.7729	198
585	CM002910	11863	13086	.	997	.	2.39178	6.02129	4.82076	1118
585	CM002910	11863	13086	.	997	.	3.62184	15.2923	13.7889	304
585	CM002910	11863	13086	.	997	.	4.92024	27.9268	26.1115	815
585	CM002910	38975	39379	.	764	.	3.75851	16.5009	14.9654	223
585	CM002910	41749	42060	.	609	.	3.05195	11.0701	9.69139	187
585	CM002910	45798	46288	.	1000	.	6.25	45.5088	43.2932	245
585	CM002910	52266	53411	.	1000	.	3.14922	15.2394	13.7413	911
585	CM002910	52266	53411	.	1000	.	7.67591	77.4808	74.5431	478
585	CM002910	57850	60187	.	1000	.	1.93108	6.39848	5.18789	147

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

Eye Discs ATAC-Seq (GSE102439_atac_eyediscs) Track Description


	Description These tracks show the results from Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq) of D. simulans eye-antennal discs from 3rd instar larvae. The peak calls and the log likelihood ratio evidence tracks were produced by MACS2. The Irreproducible Discovery Rate (IDR) peak calls were produced by the idr program using a global IDR threshold of 0.05. The datasets were obtained from the NCBI BioProject database under the accession number PRJNA397749. References Jacobs J, Atkins M, Davie K, Imrichova H, Romanelli L, Christiaens V, Hulselmans G, Potier D, Wouters J, Taskiran II, Paciello G, González-Blas CB, Koldere D, Aibar S, Halder G, Aerts S. The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes. Nat Genet. 2018 Jul;50(7):1011-1020. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.

Description