Schema for Su(H) ChIP-Seq - ChIP-Seq of Suppressor of Hairless Proteins

Database: dm6 Primary Table: GSE59726_Su_H_rabbit_ab_idr Row Count: 4,282 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5423	`int(10) unsigned`	range
`chromEnd`	6041	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.62113	`float`	range
`pValue`	24.6659	`float`	range
`qValue`	22.0128	`float`	range
`peak`	440	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5423	6041	.	1000	.	3.62113	24.6659	22.0128	440
585	chr2L	27875	28422	.	683	.	2.44169	12.4142	10.0786	220
585	chr2L	66684	67555	.	1000	.	3.2012	20.3892	17.8293	624
585	chr2L	66684	67555	.	1000	.	3.99725	43.0002	40.0269	258
585	chr2L	72312	72679	.	1000	.	2.70159	15.5308	13.0957	210
585	chr2L	90145	91128	.	909	.	1.95527	5.92945	3.90006	819
585	chr2L	90145	91128	.	909	.	2.94672	15.723	13.283	213
585	chr2L	107783	108389	.	1000	.	4.64696	49.0042	45.9438	259
585	chr2L	128635	129554	.	1000	.	1.54023	3.39274	1.59647	143
585	chr2L	128635	129554	.	1000	.	4.07411	47.065	44.0326	686

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Su(H) ChIP-Seq (SuHChIPSeq) Track Description


	Description These tracks show the results of the ChIP-Seq analyses of the Suppressor of hairless [Su(H)] protein. The regions that are enriched in the protein were identified by MACS2 and Peakzilla. 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 ChIP-Seq datasets were obtained from the Gene Expression Omnibus database at NCBI under the accession number GSE59726. References Ozdemir A, Ma L, White KP, Stathopoulos A. Su(H)-mediated repression positions gene boundaries along the dorsal-ventral axis of Drosophila embryos. Dev Cell. 2014 Oct 13;31(1):100-13. Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A. Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics. 2013 Nov 1;29(21):2705-13. 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