Schema for Architectural Proteins ChIP-Seq (S2) - ChIP-Seq of Architectural Proteins in S2 Cells

Database: dm6 Primary Table: GSE46614_Ibf1_peakzilla Row Count: 2,874 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	16901	`int(10) unsigned`	range
`chromEnd`	17269	`int(10) unsigned`	range
`name`	peakzilla_1939	`varchar(255)`	values
`score`	2	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.4	`float`	range
`pValue`	-1	`float`	range
`qValue`	0.26464	`float`	range
`peak`	184	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	16901	17269	peakzilla_1939	2	.	3.4	-1	0.26464	184
585	chr2L	35463	35831	peakzilla_296	80	.	74.06	-1	2.46852	184
585	chr2L	41974	42342	peakzilla_1036	8	.	5.78	-1	1.90658	184
585	chr2L	47219	47587	peakzilla_1907	2	.	2.75	-1	0.2898	184
585	chr2L	64788	65156	peakzilla_945	10	.	17.46	-1	1.9393	184
585	chr2L	65213	65581	peakzilla_991	9	.	6.38	-1	1.88941	184
585	chr2L	65699	66067	peakzilla_696	18	.	17.87	-1	1.9431	184
585	chr2L	72133	72501	peakzilla_1509	4	.	3.36	-1	0.99439	184
585	chr2L	73118	73486	peakzilla_347	60	.	32.56	-1	2.24413	184
585	chr2L	73819	74187	peakzilla_439	43	.	27.31	-1	2.04576	184

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Architectural Proteins ChIP-Seq (S2) (insulatorsS2ChIPSeq) Track Description

Description

These tracks show the results of the ChIP-Seq analyses of architectural proteins (also known as insulators) from S2 cells. The regions that are enriched in the architectural proteins were identified by MACS2 and Peakzilla. The log likelihood ratio evidence tracks were produced by MACS2.

The ChIP-Seq datasets were obtained from the Gene Expression Omnibus database at NCBI under the following accession numbers:

Accession	Insulators	Reference
GSE46614	Cp190, Ibf1, Ibf2	Cuartero S et al., EMBO J. 2014
GSE54337	pita, ZIPIC	Maksimenko O et al., Genome Res. 2015

References

Maksimenko O, Bartkuhn M, Stakhov V, Herold M, Zolotarev N, Jox T, Buxa MK, Kirsch R, Bonchuk A, Fedotova A, Kyrchanova O, Renkawitz R, Georgiev P. Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin. Genome Res. 2015 Jan;25(1):89-99.

Cuartero S, Fresán U, Reina O, Planet E, Espinàs ML. Ibf1 and Ibf2 are novel CP190-interacting proteins required for insulator function. EMBO J. 2014 Mar 18;33(6):637-47.

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.