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

Database: dm6 Primary Table: GSE54337_Pita_macs Row Count: 4,410 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	18589	`int(10) unsigned`	range
`chromEnd`	18708	`int(10) unsigned`	range
`name`	GSE54337_Pita_macs_peak_1	`varchar(255)`	values
`score`	349	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	9.50933	`float`	range
`pValue`	37.7551	`float`	range
`qValue`	34.9107	`float`	range
`peak`	57	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	18589	18708	GSE54337_Pita_macs_peak_1	349	.	9.50933	37.7551	34.9107	57
585	chr2L	21410	21510	GSE54337_Pita_macs_peak_2	122	.	5.3598	14.8497	12.2553	49
585	chr2L	34133	34304	GSE54337_Pita_macs_peak_3	139	.	4.65891	16.5756	13.9502	74
585	chr2L	35524	35834	GSE54337_Pita_macs_peak_4a	1375	.	21.3759	141.149	137.528	83
585	chr2L	35524	35834	GSE54337_Pita_macs_peak_4b	417	.	9.83486	44.6355	41.7427	223
585	chr2L	35890	35997	GSE54337_Pita_macs_peak_5	51	.	3.49494	7.54856	5.16207	58
585	chr2L	47164	47260	GSE54337_Pita_macs_peak_6	135	.	4.38935	16.209	13.5909	46
585	chr2L	47303	47500	GSE54337_Pita_macs_peak_7	724	.	9.00862	75.5299	72.4418	92
585	chr2L	72538	72687	GSE54337_Pita_macs_peak_8	115	.	4.1629	14.1512	11.5712	68
585	chr2L	73088	74161	GSE54337_Pita_macs_peak_9a	1494	.	17.3092	153.239	149.404	103

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.