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

Database: dm6 Primary Table: GSE54337_ZIPIC_peakzilla Row Count: 5,368 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	47092	`int(10) unsigned`	range
`chromEnd`	47314	`int(10) unsigned`	range
`name`	peakzilla_4451	`varchar(255)`	values
`score`	2	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.01	`float`	range
`pValue`	-1	`float`	range
`qValue`	1.23657	`float`	range
`peak`	111	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	47092	47314	peakzilla_4451	2	.	2.01	-1	1.23657	111
585	chr2L	47271	47493	peakzilla_3781	2	.	2.08	-1	1.49485	111
585	chr2L	66828	67050	peakzilla_2668	3	.	2.55	-1	2.25181	111
585	chr2L	73073	73295	peakzilla_1420	6	.	5.71	-1	309.653	111
585	chr2L	73768	73990	peakzilla_3694	2	.	2.7	-1	1.5391	111
585	chr2L	107791	108013	peakzilla_3604	2	.	3.01	-1	1.61798	111
585	chr2L	122348	122570	peakzilla_6785	2	.	2.34	-1	1.21325	111
585	chr2L	129235	129457	peakzilla_3053	3	.	2.57	-1	1.94692	111
586	chr2L	131978	132200	peakzilla_7515	1	.	2	-1	1.21183	111
586	chr2L	158946	159168	peakzilla_3677	2	.	2.4	-1	1.57349	111

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.