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

Database: dm6 Primary Table: GSE99004_dH1_H2Av_macs Row Count: 24,110 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	21852	`int(10) unsigned`	range
`chromEnd`	22155	`int(10) unsigned`	range
`name`	GSE99004_dH1_H2Av_macs_peak_1	`varchar(255)`	values
`score`	82	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.03955	`float`	range
`pValue`	9.94995	`float`	range
`qValue`	8.20425	`float`	range
`peak`	156	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	21852	22155	GSE99004_dH1_H2Av_macs_peak_1	82	.	2.03955	9.94995	8.20425	156
585	chr2L	73499	73894	GSE99004_dH1_H2Av_macs_peak_2	33	.	1.52243	4.7263	3.34261	83
585	chr2L	74143	75040	GSE99004_dH1_H2Av_macs_peak_3a	104	.	2.13487	12.3963	10.4936	95
585	chr2L	74143	75040	GSE99004_dH1_H2Av_macs_peak_3b	61	.	1.85461	7.78271	6.17906	322
585	chr2L	74143	75040	GSE99004_dH1_H2Av_macs_peak_3c	53	.	1.79908	6.86676	5.32552	690
585	chr2L	76813	77241	GSE99004_dH1_H2Av_macs_peak_4	36	.	1.65381	5.06267	3.6527	116
585	chr2L	77634	78103	GSE99004_dH1_H2Av_macs_peak_5a	40	.	1.714	5.45384	4.01487	139
585	chr2L	77634	78103	GSE99004_dH1_H2Av_macs_peak_5b	22	.	1.50068	3.58318	2.29929	430
585	chr2L	78515	79485	GSE99004_dH1_H2Av_macs_peak_6a	56	.	1.87642	7.21777	5.65063	111
585	chr2L	78515	79485	GSE99004_dH1_H2Av_macs_peak_6b	36	.	1.60787	5.03989	3.6317	321

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.