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

Database: dm6 Primary Table: GSE54337_ZIPIC_macs Row Count: 10,593 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	66857	`int(10) unsigned`	range
`chromEnd`	67011	`int(10) unsigned`	range
`name`	GSE54337_ZIPIC_macs_peak_1	`varchar(255)`	values
`score`	86	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.45398	`float`	range
`pValue`	11.1758	`float`	range
`qValue`	8.68272	`float`	range
`peak`	76	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	66857	67011	GSE54337_ZIPIC_macs_peak_1	86	.	2.45398	11.1758	8.68272	76
585	chr2L	73117	73256	GSE54337_ZIPIC_macs_peak_2	281	.	3.96781	31.0777	28.1156	63
585	chr2L	73800	73932	GSE54337_ZIPIC_macs_peak_3	78	.	2.48506	10.3163	7.86159	66
585	chr2L	104475	104603	GSE54337_ZIPIC_macs_peak_4	30	.	2.06289	4.96788	3.08722	60
585	chr2L	107857	107967	GSE54337_ZIPIC_macs_peak_5	116	.	3.18276	14.2155	11.615	52
585	chr2L	118455	118580	GSE54337_ZIPIC_macs_peak_6	45	.	2.33552	6.77212	4.58956	56
585	chr2L	129087	129417	GSE54337_ZIPIC_macs_peak_7a	31	.	1.81462	5.1011	3.19864	37
585	chr2L	129087	129417	GSE54337_ZIPIC_macs_peak_7b	75	.	2.37451	10.0289	7.58768	180
586	chr2L	131984	132139	GSE54337_ZIPIC_macs_peak_8	80	.	2.74926	10.5093	8.04619	87
586	chr2L	158987	159297	GSE54337_ZIPIC_macs_peak_9a	92	.	2.67569	11.8175	9.29892	72

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.