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

Database: dm6 Primary Table: GSE46614_CP190_peakzilla Row Count: 6,811 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	18454	`int(10) unsigned`	range
`chromEnd`	18842	`int(10) unsigned`	range
`name`	peakzilla_6326	`varchar(255)`	values
`score`	53	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	158.9	`float`	range
`pValue`	-1	`float`	range
`qValue`	0.12831	`float`	range
`peak`	194	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	18454	18842	peakzilla_6326	53	.	158.9	-1	0.12831	194
585	chr2L	35461	35849	peakzilla_6288	73	.	65.03	-1	0.12767	194
585	chr2L	42004	42392	peakzilla_6977	4	.	3.24	-1	0.1396	194
585	chr2L	47210	47598	peakzilla_6374	40	.	14.7	-1	0.12919	194
585	chr2L	64717	65105	peakzilla_7039	3	.	10.66	-1	0.14068	194
585	chr2L	65201	65589	peakzilla_7070	2	.	2.41	-1	0.14122	194
585	chr2L	65680	66068	peakzilla_6451	24	.	21.98	-1	0.13053	194
585	chr2L	72158	72546	peakzilla_6801	6	.	4.06	-1	0.13662	194
585	chr2L	73077	73465	peakzilla_96	367	.	218.43	-1	309.653	194
585	chr2L	73757	74145	peakzilla_6241	127	.	65.56	-1	0.12685	194

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.