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

Database: DvirCAF1 Primary Table: GSE102439_eyediscs_idr Row Count: 13,802 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_10111	`varchar(255)`	values
`chromStart`	4246	`int(10) unsigned`	range
`chromEnd`	4624	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	575	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	5.17433	`float`	range
`pValue`	21.6462	`float`	range
`qValue`	19.8292	`float`	range
`peak`	174	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	scaffold_10111	4246	4624	.	575	.	5.17433	21.6462	19.8292	174
585	scaffold_10277	35	1034	.	1000	.	4.15976	14.4311	12.8186	245
585	scaffold_10277	35	1034	.	1000	.	5.47871	23.9819	22.1036	498
585	scaffold_10277	35	1034	.	1000	.	8.62389	51.7323	49.1793	814
585	scaffold_10304	5346	5693	.	922	.	5.27579	22.4166	20.5792	195
585	scaffold_10322	41208	41849	.	1000	.	9.13118	56.7209	54.048	364
585	scaffold_10322	57586	58387	.	548	.	2.31405	4.83126	3.58971	521
585	scaffold_10322	57586	58387	.	548	.	4.18569	18.6384	16.9072	146
585	scaffold_10322	63595	64142	.	828	.	5.77381	42.4991	40.1713	355
585	scaffold_10322	69690	70027	.	798	.	5.16507	38.3748	36.1469	177

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. virilis 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