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

Database: DpseGB3 Primary Table: GSE102439_eyediscs_idr_nextseq Row Count: 25,757 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CH379058	`varchar(255)`	values
`chromStart`	6472	`int(10) unsigned`	range
`chromEnd`	7035	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	829	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.99284	`float`	range
`pValue`	13.2406	`float`	range
`qValue`	11.6815	`float`	range
`peak`	175	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	CH379058	6472	7035	.	829	.	2.99284	13.2406	11.6815	175
585	CH379058	47826	48287	.	775	.	2.87162	13.8889	12.309	192
585	CH379058	68185	68900	.	1000	.	1.89655	4.5391	3.35128	566
585	CH379058	68185	68900	.	1000	.	6.44748	70.6574	67.4228	246
585	CH379058	70647	71303	.	729	.	2.40709	8.97334	7.57457	265
585	CH379058	70647	71303	.	729	.	2.8481	14.4195	12.822	532
585	CH379058	71884	72192	.	958	.	3.37644	23.2438	21.3798	158
585	CH379058	75750	76350	.	765	.	3.07956	16.1587	14.5061	281
585	CH379058	82017	82448	.	848	.	2.89308	12.2448	10.7199	229
585	CH379058	88773	89144	.	560	.	2.5938	9.43604	8.01416	228

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. pseudoobscura 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