Schema for Histone Variants ChIP-Seq (S2) - ChIP-Seq of Histone Variants in S2 Cells

Database: dm6 Primary Table: GSE99004_wt_H2Av_idr Row Count: 19,958 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	21554	`int(10) unsigned`	range
`chromEnd`	22776	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	580	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	1.58973	`float`	range
`pValue`	4.10163	`float`	range
`qValue`	2.85209	`float`	range
`peak`	1032	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	21554	22776	.	580	.	1.58973	4.10163	2.85209	1032
585	chr2L	21554	22776	.	580	.	2.16232	10.7383	9.12956	110
585	chr2L	21554	22776	.	580	.	2.2038	12.61	10.9145	454
585	chr2L	21554	22776	.	580	.	1.26944	1.72557	0.69871	853
585	chr2L	73405	75571	.	629	.	2.18017	13.0859	11.3696	1062
585	chr2L	73405	75571	.	629	.	2.59474	22.4513	20.2803	819
585	chr2L	73405	75571	.	629	.	2.33539	15.6525	13.8194	1490
585	chr2L	73405	75571	.	629	.	1.299	1.81125	0.77212	2098
585	chr2L	73405	75571	.	629	.	1.5674	4.92683	3.62204	612
585	chr2L	73405	75571	.	629	.	1.91918	11.0402	9.4164	299

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Histone Variants ChIP-Seq (S2) (variantsChIPSeq) Track Description

Description

These tracks show the results of the ChIP-Seq analyses of histone variants from S2 cells. The regions that are enriched in histone variants were identified by MACS2 and Peakzilla. 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 Gene Expression Omnibus database at NCBI under the following accession numbers:

Accession	Proteins	Reference
GSE99004	H2Av, H2Av dH1 RNAi	Bayona-Feliu A et al., Nat Commun. 2017

References

Bayona-Feliu A, Casas-Lamesa A, Reina O, Bernués J, Azorin F. Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin. Nat Commun. 2017 Aug 18;8(1):283.

Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A. Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics. 2013 Nov 1;29(21):2705-13.

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.