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

Database: dm6 Primary Table: GSE85191_H3K4me1_macs Row Count: 34,675 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	4970	`int(10) unsigned`	range
`chromEnd`	7096	`int(10) unsigned`	range
`name`	GSE85191_H3K4me1_macs_peak_1a	`varchar(255)`	values
`score`	674	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.59519	`float`	range
`pValue`	70.0871	`float`	range
`qValue`	67.4966	`float`	range
`peak`	409	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	4970	7096	GSE85191_H3K4me1_macs_peak_1a	674	.	2.59519	70.0871	67.4966	409
585	chr2L	4970	7096	GSE85191_H3K4me1_macs_peak_1b	542	.	2.36397	56.4741	54.209	1669
585	chr2L	7445	9359	GSE85191_H3K4me1_macs_peak_2a	415	.	2.09101	43.4541	41.5018	381
585	chr2L	7445	9359	GSE85191_H3K4me1_macs_peak_2b	213	.	1.71651	22.769	21.3229	1481
585	chr2L	13747	15705	GSE85191_H3K4me1_macs_peak_3a	273	.	1.93501	28.9688	27.3652	776
585	chr2L	13747	15705	GSE85191_H3K4me1_macs_peak_3b	229	.	1.83012	24.4195	22.9309	1425
585	chr2L	16233	16681	GSE85191_H3K4me1_macs_peak_4	171	.	1.70696	18.498	17.1649	162
585	chr2L	16980	17252	GSE85191_H3K4me1_macs_peak_5	202	.	1.7775	21.6966	20.2783	125
585	chr2L	18796	19374	GSE85191_H3K4me1_macs_peak_6	243	.	1.93933	25.8648	24.3392	400
585	chr2L	19705	20335	GSE85191_H3K4me1_macs_peak_7a	258	.	2.05034	27.4452	25.8803	194

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