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

Database: dm6 Primary Table: GSE85191_H3K4me3_idr Row Count: 15,914 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5067	`int(10) unsigned`	range
`chromEnd`	9394	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	1.27492	`float`	range
`pValue`	3.42304	`float`	range
`qValue`	2.34949	`float`	range
`peak`	2124	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5067	9394	.	1000	.	1.27492	3.42304	2.34949	2124
585	chr2L	5067	9394	.	1000	.	1.75841	19.0708	17.3285	2742
585	chr2L	5067	9394	.	1000	.	1.46195	9.26663	7.85982	3813
585	chr2L	5067	9394	.	1000	.	1.88069	22.5536	20.6959	1394
585	chr2L	5067	9394	.	1000	.	2.00223	28.121	26.0739	337
585	chr2L	18274	18604	.	1000	.	1.54285	12.9561	11.4187	185
585	chr2L	19810	20831	.	1000	.	1.44589	8.90203	7.50934	469
585	chr2L	19810	20831	.	1000	.	1.72922	20.2157	18.4359	820
585	chr2L	45925	47352	.	1000	.	1.79114	18.7864	17.0537	233
585	chr2L	45925	47352	.	1000	.	2.18135	37.2215	34.8597	950

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