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

Database: dm6 Primary Table: GSE99004_dH1_H2Av_idr Row Count: 23,930 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	21562	`int(10) unsigned`	range
`chromEnd`	22162	`int(10) unsigned`	range
`name`	.	`varchar(255)`	values
`score`	703	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.08615	`float`	range
`pValue`	9.09254	`float`	range
`qValue`	7.38904	`float`	range
`peak`	446	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	21562	22162	.	703	.	2.08615	9.09254	7.38904	446
585	chr2L	21562	22162	.	703	.	1.7549	4.74325	3.34162	92
585	chr2L	66558	66791	.	890	.	2.0527	9.84474	8.09463	135
585	chr2L	73437	75554	.	1000	.	1.99563	7.73608	6.11853	1396
585	chr2L	73437	75554	.	1000	.	2.08187	8.79856	7.11397	1028
585	chr2L	73437	75554	.	1000	.	2.43044	13.8511	11.8498	801
585	chr2L	73437	75554	.	1000	.	1.75793	6.58893	5.05017	145
585	chr2L	73437	75554	.	1000	.	1.17944	1.08949	0.13075	1803
585	chr2L	73437	75554	.	1000	.	1.53474	2.99935	1.75964	2023
585	chr2L	77436	78326	.	578	.	1.74161	4.90092	3.48788	337

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.