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

Database: DpseGB3 Primary Table: GSE102439_eyediscs_macs_nextseq Row Count: 30,088 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CH379058	`varchar(255)`	values
`chromStart`	6510	`int(10) unsigned`	range
`chromEnd`	6806	`int(10) unsigned`	range
`name`	GSE102439_DpseGB3_atac_next...	`varchar(255)`	values
`score`	116	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.99284	`float`	range
`pValue`	13.2406	`float`	range
`qValue`	11.6815	`float`	range
`peak`	137	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	CH379058	6510	6806	GSE102439_DpseGB3_atac_nextseq_macs_peak_1	116	.	2.99284	13.2406	11.6815	137
585	CH379058	36766	37327	GSE102439_DpseGB3_atac_nextseq_macs_peak_2	111	.	2.94296	12.7391	11.1971	335
585	CH379058	43823	44072	GSE102439_DpseGB3_atac_nextseq_macs_peak_3	52	.	2.1838	6.52052	5.23018	108
585	CH379058	47845	48266	GSE102439_DpseGB3_atac_nextseq_macs_peak_4	123	.	2.87162	13.8889	12.309	173
585	CH379058	55456	55752	GSE102439_DpseGB3_atac_nextseq_macs_peak_5	45	.	2.14487	5.77897	4.51943	113
585	CH379058	55825	56046	GSE102439_DpseGB3_atac_nextseq_macs_peak_6	41	.	2.09499	5.4181	4.17751	106
585	CH379058	68216	68833	GSE102439_DpseGB3_atac_nextseq_macs_peak_7	674	.	6.44748	70.6574	67.4228	215
585	CH379058	70806	71279	GSE102439_DpseGB3_atac_nextseq_macs_peak_8a	75	.	2.40709	8.97334	7.57457	106
585	CH379058	70806	71279	GSE102439_DpseGB3_atac_nextseq_macs_peak_8b	128	.	2.8481	14.4195	12.822	373
585	CH379058	71904	72179	GSE102439_DpseGB3_atac_nextseq_macs_peak_9	213	.	3.37644	23.2438	21.3798	138

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