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

Database: DpseGB3 Primary Table: GSE102439_eyediscs_macs_hiseq Row Count: 24,585 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CH379058	`varchar(255)`	values
`chromStart`	43700	`int(10) unsigned`	range
`chromEnd`	43904	`int(10) unsigned`	range
`name`	GSE102439_DpseGB3_atac_hise...	`varchar(255)`	values
`score`	38	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.58492	`float`	range
`pValue`	5.18106	`float`	range
`qValue`	3.88258	`float`	range
`peak`	109	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	CH379058	43700	43904	GSE102439_DpseGB3_atac_hiseq_macs_peak_1	38	.	2.58492	5.18106	3.88258	109
585	CH379058	68233	68642	GSE102439_DpseGB3_atac_hiseq_macs_peak_2	812	.	10.7266	84.7914	81.2811	191
585	CH379058	71047	71291	GSE102439_DpseGB3_atac_hiseq_macs_peak_3	237	.	5.19263	25.7474	23.784	131
585	CH379058	71946	72175	GSE102439_DpseGB3_atac_hiseq_macs_peak_4	164	.	4.16025	18.2234	16.4675	114
585	CH379058	82177	82472	GSE102439_DpseGB3_atac_hiseq_macs_peak_5	38	.	2.58492	5.18106	3.88258	106
585	CH379058	86311	86531	GSE102439_DpseGB3_atac_hiseq_macs_peak_6	38	.	2.58492	5.18106	3.88258	120
585	CH379058	93886	94305	GSE102439_DpseGB3_atac_hiseq_macs_peak_7	137	.	4.4159	15.3784	13.7018	292
585	CH379058	115814	116451	GSE102439_DpseGB3_atac_hiseq_macs_peak_8a	69	.	3.23115	8.34011	6.90117	148
585	CH379058	115814	116451	GSE102439_DpseGB3_atac_hiseq_macs_peak_8b	299	.	6.6777	32.1018	29.972	450
585	CH379058	123918	124395	GSE102439_DpseGB3_atac_hiseq_macs_peak_9	87	.	3.47222	10.2997	8.78916	183

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