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

Database: dm6 Primary Table: GSE46614_Ibf2_macs Row Count: 2,773 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	19457	`int(10) unsigned`	range
`chromEnd`	19921	`int(10) unsigned`	range
`name`	GSE46614_Ibf2_macs_peak_1	`varchar(255)`	values
`score`	397	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	8.75117	`float`	range
`pValue`	42.2522	`float`	range
`qValue`	39.7739	`float`	range
`peak`	153	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	19457	19921	GSE46614_Ibf2_macs_peak_1	397	.	8.75117	42.2522	39.7739	153
585	chr2L	35209	35957	GSE46614_Ibf2_macs_peak_2	3162	.	28.4839	319.683	316.278	422
585	chr2L	41801	42549	GSE46614_Ibf2_macs_peak_3	286	.	6.7773	31.1076	28.6996	314
585	chr2L	64791	66110	GSE46614_Ibf2_macs_peak_4a	319	.	7.70626	34.4117	31.9804	179
585	chr2L	64791	66110	GSE46614_Ibf2_macs_peak_4b	500	.	10.0402	52.5661	50.0344	593
585	chr2L	64791	66110	GSE46614_Ibf2_macs_peak_4c	1231	.	17.7501	125.935	123.13	1068
585	chr2L	72205	72569	GSE46614_Ibf2_macs_peak_5	61	.	3.08978	8.26488	6.13086	185
585	chr2L	72986	74658	GSE46614_Ibf2_macs_peak_6a	1900	.	16.619	193.038	190.028	321
585	chr2L	72986	74658	GSE46614_Ibf2_macs_peak_6b	1987	.	18.4252	201.772	198.737	1012
585	chr2L	102218	102568	GSE46614_Ibf2_macs_peak_7	55	.	3.2109	7.63967	5.52337	101

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.