Schema for Henriques 2018 ChIP-Seq - ChIP-Seq Data from Henriques 2018 for S2 cells

Database: dm6 Primary Table: GSE85191_PolII_idr Row Count: 12,319 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	8435	`int(10) unsigned`	range
`chromEnd`	9737	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	650	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	1.20298	`float`	range
`pValue`	1.44726	`float`	range
`qValue`	0.27499	`float`	range
`peak`	1260	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	8435	9737	.	650	.	1.20298	1.44726	0.27499	1260
585	chr2L	8435	9737	.	650	.	1.4285	3.46275	2.03018	212
585	chr2L	8435	9737	.	650	.	1.52275	4.97658	3.44686	937
585	chr2L	8435	9737	.	650	.	2.06073	14.6046	12.7996	463
585	chr2L	18292	19221	.	1000	.	4.10246	80.2734	77.7413	339
585	chr2L	19536	19942	.	908	.	2.136	14.2157	12.4182	211
585	chr2L	45949	47465	.	807	.	1.95588	5.76919	4.20097	238
585	chr2L	45949	47465	.	807	.	1.99144	6.0907	4.5087	790
585	chr2L	45949	47465	.	807	.	2.027	6.4196	4.82434	642
585	chr2L	45949	47465	.	807	.	2.27593	8.9194	7.24178	1076

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

Henriques 2018 ChIP-Seq (henriques2018ChIPSeq) Track Description


	Description These tracks show the analysis results for the ChIP-Seq data produced by Henriques and colleagues (PMID: 29378787). The regions that are enriched in the histone modifications and chromosomal proteins were identified by MACS2. 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 NCBI Gene Expression Omnibus database under the accession number GSE85191. References Henriques T, Scruggs BS, Inouye MO, Muse GW, Williams LH, Burkholder AB, Lavender CA, Fargo DC, Adelman K. Widespread transcriptional pausing and elongation control at enhancers. Genes Dev. 2018 Jan 1;32(1):26-41. 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