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

Database: DereCAF1 Primary Table: GSE102439_eyediscs_idr Row Count: 22,846 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_1211	`varchar(255)`	values
`chromStart`	163	`int(10) unsigned`	range
`chromEnd`	433	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	4.35088	`float`	range
`pValue`	42.98	`float`	range
`qValue`	40.4298	`float`	range
`peak`	136	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	scaffold_1211	163	433	.	1000	.	4.35088	42.98	40.4298	136
585	scaffold_1256	278	1033	.	770	.	2.27432	9.48862	7.99335	120
585	scaffold_1256	278	1033	.	770	.	2.07656	7.3282	5.92771	467
585	scaffold_1299	0	343	.	1000	.	5.6034	70.0557	66.6555	143
585	scaffold_1383	3987	5183	.	1000	.	1.45029	2.16613	1.12779	1076
585	scaffold_1383	3987	5183	.	1000	.	5.30675	63.2772	60.093	526
585	scaffold_1390	154	731	.	1000	.	8.73472	152.502	145.781	238
585	scaffold_1390	8165	8427	.	1000	.	4.08719	37.841	35.4452	129
585	scaffold_1390	9080	9327	.	1000	.	3.69165	30.5536	28.3761	122
585	scaffold_1390	15464	16542	.	1000	.	7.61404	120.957	115.8	848

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. erecta 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