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

Database: dm6 Primary Table: GSE85191_H3K4me3_macs Row Count: 22,069 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	5115	`int(10) unsigned`	range
`chromEnd`	6964	`int(10) unsigned`	range
`name`	GSE85191_H3K4me3_macs_peak_1b	`varchar(255)`	values
`score`	206	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	1.88069	`float`	range
`pValue`	22.5536	`float`	range
`qValue`	20.6959	`float`	range
`peak`	1346	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	5115	6964	GSE85191_H3K4me3_macs_peak_1b	206	.	1.88069	22.5536	20.6959	1346
585	chr2L	5115	6964	GSE85191_H3K4me3_macs_peak_1a	260	.	2.00223	28.121	26.0739	289
585	chr2L	7498	8209	GSE85191_H3K4me3_macs_peak_2	173	.	1.75841	19.0708	17.3285	311
585	chr2L	8450	9057	GSE85191_H3K4me3_macs_peak_3	78	.	1.46195	9.26663	7.85982	430
585	chr2L	17502	17780	GSE85191_H3K4me3_macs_peak_4	48	.	1.34369	6.11255	4.84374	115
585	chr2L	18297	18566	GSE85191_H3K4me3_macs_peak_5	117	.	1.55219	13.3397	11.7891	171
585	chr2L	19854	20798	GSE85191_H3K4me3_macs_peak_6a	75	.	1.44589	8.90203	7.50934	425
585	chr2L	19854	20798	GSE85191_H3K4me3_macs_peak_6b	184	.	1.72922	20.2157	18.4359	776
585	chr2L	22139	22448	GSE85191_H3K4me3_macs_peak_7	47	.	1.35758	6.00226	4.73981	156
585	chr2L	45973	47329	GSE85191_H3K4me3_macs_peak_8a	170	.	1.79114	18.7864	17.0537	185

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