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

Database: dm6 Primary Table: GSE85191_PolII_macs Row Count: 13,063 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5255	`int(10) unsigned`	range
`chromEnd`	5864	`int(10) unsigned`	range
`name`	GSE85191_PolII_macs_peak_1a	`varchar(255)`	values
`score`	24	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	1.60548	`float`	range
`pValue`	3.91236	`float`	range
`qValue`	2.44573	`float`	range
`peak`	91	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5255	5864	GSE85191_PolII_macs_peak_1a	24	.	1.60548	3.91236	2.44573	91
585	chr2L	5255	5864	GSE85191_PolII_macs_peak_1b	41	.	1.7597	5.685	4.12179	402
585	chr2L	7750	8117	GSE85191_PolII_macs_peak_2	76	.	1.87386	9.35903	7.66937	140
585	chr2L	8522	9098	GSE85191_PolII_macs_peak_3b	127	.	2.06073	14.6046	12.7996	376
585	chr2L	8522	9098	GSE85191_PolII_macs_peak_3a	20	.	1.4285	3.46275	2.03018	126
585	chr2L	12983	13208	GSE85191_PolII_macs_peak_4	82	.	1.78719	10.0014	8.29565	108
585	chr2L	18308	19178	GSE85191_PolII_macs_peak_5	777	.	4.10246	80.2734	77.7413	323
585	chr2L	19566	19915	GSE85191_PolII_macs_peak_6	124	.	2.136	14.2157	12.4182	181
585	chr2L	46075	46271	GSE85191_PolII_macs_peak_7	45	.	1.99144	6.0907	4.5087	116
585	chr2L	46456	47392	GSE85191_PolII_macs_peak_8a	48	.	2.027	6.4196	4.82434	135

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