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

Database: dm6 Primary Table: GSE54337_Pita_peakzilla Row Count: 6,458 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	34120	`int(10) unsigned`	range
`chromEnd`	34318	`int(10) unsigned`	range
`name`	peakzilla_2134	`varchar(255)`	values
`score`	5	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	5.33	`float`	range
`pValue`	-1	`float`	range
`qValue`	3.30103	`float`	range
`peak`	99	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	34120	34318	peakzilla_2134	5	.	5.33	-1	3.30103	99
585	chr2L	35510	35708	peakzilla_739	37	.	46.53	-1	309.653	99
585	chr2L	35838	36036	peakzilla_4666	2	.	2.76	-1	1.41229	99
585	chr2L	47299	47497	peakzilla_1033	20	.	11.96	-1	3	99
585	chr2L	72281	72479	peakzilla_4760	2	.	3.01	-1	1.37263	99
585	chr2L	72515	72713	peakzilla_2875	3	.	2.91	-1	2.85387	99
585	chr2L	73096	73294	peakzilla_475	80	.	65.57	-1	309.653	99
585	chr2L	73792	73990	peakzilla_582	58	.	51.02	-1	309.653	99
585	chr2L	102214	102412	peakzilla_511	72	.	44.9	-1	309.653	99
585	chr2L	106152	106350	peakzilla_5978	2	.	2.2	-1	0.91222	99

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.