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

Database: dm6 Primary Table: GSE85191_PolII_Spt5depleted_idr Row Count: 12,450 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	18257	`int(10) unsigned`	range
`chromEnd`	19217	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.7549	`float`	range
`pValue`	62.0443	`float`	range
`qValue`	59.5608	`float`	range
`peak`	369	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	18257	19217	.	1000	.	3.7549	62.0443	59.5608	369
585	chr2L	45962	47438	.	1000	.	2.03442	6.47019	4.86085	307
585	chr2L	45962	47438	.	1000	.	2.74825	14.4753	12.6442	851
585	chr2L	45962	47438	.	1000	.	2.81963	15.4073	13.5569	1197
585	chr2L	45962	47438	.	1000	.	2.89102	16.3608	14.4917	1307
585	chr2L	52614	53410	.	1000	.	2.64117	13.1189	11.3171	229
585	chr2L	52614	53410	.	1000	.	2.74825	14.4753	12.6442	575
585	chr2L	66906	67395	.	1000	.	5.68869	104.438	101.482	187
585	chr2L	72229	74742	.	1000	.	1.56418	5.74851	4.17141	2084
585	chr2L	72229	74742	.	1000	.	1.67683	7.57199	5.92164	138

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