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

Database: dm6 Primary Table: GSE46614_Ibf2_peakzilla Row Count: 3,436 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	35446	`int(10) unsigned`	range
`chromEnd`	35810	`int(10) unsigned`	range
`name`	peakzilla_382	`varchar(255)`	values
`score`	103	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	95.3	`float`	range
`pValue`	-1	`float`	range
`qValue`	2.58503	`float`	range
`peak`	182	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	35446	35810	peakzilla_382	103	.	95.3	-1	2.58503	182
585	chr2L	41925	42289	peakzilla_1541	9	.	5.88	-1	2.14874	182
585	chr2L	47223	47587	peakzilla_2056	5	.	2.84	-1	1.67778	182
585	chr2L	64783	65147	peakzilla_1323	12	.	20.03	-1	2.12494	182
585	chr2L	65187	65551	peakzilla_1203	14	.	10.06	-1	2.13077	182
585	chr2L	65674	66038	peakzilla_814	30	.	35.61	-1	2.21467	182
585	chr2L	72153	72517	peakzilla_2509	3	.	2.86	-1	0.91009	182
585	chr2L	73126	73490	peakzilla_512	68	.	35.81	-1	2.72125	182
585	chr2L	73828	74192	peakzilla_589	54	.	35.54	-1	2.29243	182
585	chr2L	87856	88220	peakzilla_4512	1	.	2.27	-1	0.11345	182

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.