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

Database: dm6 Primary Table: GSE99004_wt_H2Av_peakzilla Row Count: 14,454 Data last updated: 2021-09-01

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	21498	`int(10) unsigned`	range
`chromEnd`	21840	`int(10) unsigned`	range
`name`	peakzilla_14860	`varchar(255)`	values
`score`	2	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.55	`float`	range
`pValue`	-1	`float`	range
`qValue`	0.70137	`float`	range
`peak`	171	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	21498	21840	peakzilla_14860	2	.	2.55	-1	0.70137	171
585	chr2L	21854	22196	peakzilla_14248	2	.	2.56	-1	0.74934	171
585	chr2L	66988	67330	peakzilla_9265	3	.	2.6	-1	1.16178	171
585	chr2L	71001	71343	peakzilla_18388	1	.	2.09	-1	0.49526	171
585	chr2L	71887	72229	peakzilla_12130	2	.	3.07	-1	0.91328	171
585	chr2L	72784	73126	peakzilla_10372	3	.	2.32	-1	1.05502	171
585	chr2L	73513	73855	peakzilla_10406	3	.	2.58	-1	1.04964	171
585	chr2L	74037	74379	peakzilla_9119	3	.	2.64	-1	1.18046	171
585	chr2L	74734	75076	peakzilla_13153	2	.	2.59	-1	0.83239	171
585	chr2L	79163	79505	peakzilla_11142	2	.	2.98	-1	0.9974	171

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.