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

Database: DpseGB3 Primary Table: GSE102439_eyediscs_idr_hiseq Row Count: 19,882 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CH379058	`varchar(255)`	values
`chromStart`	68209	`int(10) unsigned`	range
`chromEnd`	68838	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	10.7266	`float`	range
`pValue`	84.7914	`float`	range
`qValue`	81.2811	`float`	range
`peak`	215	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	CH379058	68209	68838	.	1000	.	10.7266	84.7914	81.2811	215
585	CH379058	70791	71354	.	1000	.	2.33969	4.79758	3.52053	110
585	CH379058	70791	71354	.	1000	.	5.19263	25.7474	23.784	387
585	CH379058	71930	72188	.	832	.	4.16025	18.2234	16.4675	130
585	CH379058	93857	94385	.	768	.	4.4159	15.3784	13.7018	321
585	CH379058	115758	116721	.	1000	.	2.04639	3.01246	1.84521	947
585	CH379058	115758	116721	.	1000	.	3.23115	8.34011	6.90117	204
585	CH379058	115758	116721	.	1000	.	6.6777	32.1018	29.972	506
586	CH379058	147316	148719	.	1000	.	3.96967	26.9597	24.962	209
586	CH379058	147316	148719	.	1000	.	4.21525	30.3093	28.2276	1128

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