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

Database: dm6 Primary Table: GSE85191_H3K4me1_idr Row Count: 32,448 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	4956	`int(10) unsigned`	range
`chromEnd`	7256	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.59519	`float`	range
`pValue`	70.0871	`float`	range
`qValue`	67.4966	`float`	range
`peak`	423	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	4956	7256	.	1000	.	2.59519	70.0871	67.4966	423
585	chr2L	4956	7256	.	1000	.	2.36397	56.4741	54.209	1683
585	chr2L	7403	9401	.	1000	.	1.71651	22.769	21.3229	1523
585	chr2L	7403	9401	.	1000	.	2.09101	43.4541	41.5018	423
585	chr2L	13690	15756	.	1000	.	1.83012	24.4195	22.9309	1482
585	chr2L	13690	15756	.	1000	.	1.93501	28.9688	27.3652	833
585	chr2L	16209	16737	.	998	.	1.70696	18.498	17.1649	186
585	chr2L	16954	17275	.	970	.	1.7775	21.6966	20.2783	151
585	chr2L	18756	19405	.	1000	.	1.93933	25.8648	24.3392	440
585	chr2L	19568	20374	.	1000	.	1.4322	5.89275	4.93429	651

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