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

Database: dm6 Primary Table: GSE99004_dH1_H2Av_peakzilla Row Count: 13,434 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	21471	`int(10) unsigned`	range
`chromEnd`	21827	`int(10) unsigned`	range
`name`	peakzilla_14976	`varchar(255)`	values
`score`	2	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.76	`float`	range
`pValue`	-1	`float`	range
`qValue`	0.56575	`float`	range
`peak`	178	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	21471	21827	peakzilla_14976	2	.	2.76	-1	0.56575	178
585	chr2L	66524	66880	peakzilla_9355	3	.	2.69	-1	0.95311	178
585	chr2L	66976	67332	peakzilla_15228	2	.	2.04	-1	0.55021	178
585	chr2L	71866	72222	peakzilla_12360	2	.	3.56	-1	0.73189	178
585	chr2L	72798	73154	peakzilla_12124	2	.	2.18	-1	0.74618	178
585	chr2L	74044	74400	peakzilla_9927	2	.	2.75	-1	0.90483	178
585	chr2L	74691	75047	peakzilla_14463	2	.	2.54	-1	0.59397	178
585	chr2L	76766	77122	peakzilla_17892	1	.	2.08	-1	0.44563	178
585	chr2L	78424	78780	peakzilla_15678	2	.	2.56	-1	0.52549	178
585	chr2L	79199	79555	peakzilla_16811	2	.	2.06	-1	0.48386	178

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.