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

Database: dm6 Primary Table: GSE85191_Cohesin_macs Row Count: 20,926 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5195	`int(10) unsigned`	range
`chromEnd`	5449	`int(10) unsigned`	range
`name`	GSE85191_Cohesin_macs_peak_1	`varchar(255)`	values
`score`	42	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	1.54948	`float`	range
`pValue`	6.23881	`float`	range
`qValue`	4.22636	`float`	range
`peak`	118	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5195	5449	GSE85191_Cohesin_macs_peak_1	42	.	1.54948	6.23881	4.22636	118
585	chr2L	5646	6006	GSE85191_Cohesin_macs_peak_2	51	.	1.60603	7.28522	5.10305	177
585	chr2L	6386	6656	GSE85191_Cohesin_macs_peak_3a	40	.	1.53817	6.03856	4.0612	62
585	chr2L	6386	6656	GSE85191_Cohesin_macs_peak_3b	26	.	1.42507	4.20695	2.60674	240
585	chr2L	6714	6871	GSE85191_Cohesin_macs_peak_4	56	.	1.63996	7.94854	5.67111	91
585	chr2L	7543	8025	GSE85191_Cohesin_macs_peak_5a	60	.	1.66258	8.4052	6.06654	185
585	chr2L	7543	8025	GSE85191_Cohesin_macs_peak_5b	79	.	1.76437	10.5998	7.99946	358
585	chr2L	8229	8368	GSE85191_Cohesin_macs_peak_6	33	.	1.48322	5.19841	3.38874	66
585	chr2L	8419	8597	GSE85191_Cohesin_macs_peak_7	22	.	1.37846	3.69907	2.23198	162
585	chr2L	8773	9003	GSE85191_Cohesin_macs_peak_8	60	.	1.62566	8.35545	6.0327	133

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