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

Database: dm6 Primary Table: GSE99004_wt_H2Av_macs Row Count: 26,781 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	21566	`int(10) unsigned`	range
`chromEnd`	21750	`int(10) unsigned`	range
`name`	GSE99004_wt_H2Av_macs_peak_1	`varchar(255)`	values
`score`	91	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.16232	`float`	range
`pValue`	10.7383	`float`	range
`qValue`	9.12956	`float`	range
`peak`	98	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	21566	21750	GSE99004_wt_H2Av_macs_peak_1	91	.	2.16232	10.7383	9.12956	98
585	chr2L	21861	22159	GSE99004_wt_H2Av_macs_peak_2	109	.	2.2038	12.61	10.9145	147
585	chr2L	22472	22648	GSE99004_wt_H2Av_macs_peak_3	31	.	1.61533	4.40691	3.13655	123
585	chr2L	52719	52921	GSE99004_wt_H2Av_macs_peak_4	30	.	1.52176	4.32473	3.0595	127
585	chr2L	53010	53177	GSE99004_wt_H2Av_macs_peak_5	37	.	1.59539	5.09817	3.78196	116
585	chr2L	67067	67238	GSE99004_wt_H2Av_macs_peak_6	83	.	1.79433	9.95733	8.38458	92
585	chr2L	67434	67632	GSE99004_wt_H2Av_macs_peak_7	52	.	1.64854	6.67005	5.26119	83
585	chr2L	69249	69555	GSE99004_wt_H2Av_macs_peak_8	54	.	1.72402	6.90001	5.47965	139
585	chr2L	69801	70114	GSE99004_wt_H2Av_macs_peak_9	48	.	1.65399	6.18448	4.80346	81
585	chr2L	71482	71892	GSE99004_wt_H2Av_macs_peak_10a	38	.	1.63803	5.21092	3.88849	103

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.