Schema for Architectural Proteins ChIP-Seq (Kc167) - ChIP-Seq of Architectural Proteins in Kc167 Cells

Database: dm6 Primary Table: BEAF_interphase_macs Row Count: 7,643 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	65767	`int(10) unsigned`	range
`chromEnd`	65965	`int(10) unsigned`	range
`name`	BEAF_interphase_macs_peak_1	`varchar(255)`	values
`score`	513	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	18.1507	`float`	range
`pValue`	53.822	`float`	range
`qValue`	51.3393	`float`	range
`peak`	102	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	65767	65965	BEAF_interphase_macs_peak_1	513	.	18.1507	53.822	51.3393	102
585	chr2L	72010	72336	BEAF_interphase_macs_peak_2	487	.	15.9461	51.2135	48.7447	134
585	chr2L	72579	72800	BEAF_interphase_macs_peak_3	329	.	9.68354	35.2819	32.9046	102
585	chr2L	73115	73510	BEAF_interphase_macs_peak_4	1858	.	27.3444	189.177	185.819	234
585	chr2L	73850	73949	BEAF_interphase_macs_peak_5	31	.	3.23068	5.16664	3.18054	56
585	chr2L	74277	74401	BEAF_interphase_macs_peak_6	103	.	6.09172	12.5578	10.3947	59
585	chr2L	94640	94853	BEAF_interphase_macs_peak_7	1300	.	27.8953	132.942	130.058	99
585	chr2L	102166	102581	BEAF_interphase_macs_peak_8	2508	.	46.661	255.802	250.882	170
585	chr2L	106664	106812	BEAF_interphase_macs_peak_9	265	.	8.94912	28.8818	26.5503	77
585	chr2L	114487	114820	BEAF_interphase_macs_peak_10	1930	.	28.3676	196.464	193.01	129

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Architectural Proteins ChIP-Seq (Kc167) (insulatorsChIPSeq) Track Description

Description

These tracks show the results of the ChIP-Seq analyses of architectural proteins (also known as insulators) from Kc167 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
GSE32584	BEAF-32, Cp190, CTCF	Yang J et al., Nat Commun. 2013
GSE39521	Myc	Yang J et al., Nat Commun. 2013
GSE39664	Dref	Gurudatta BV et al., Cell Cycle. 2013
GSE62904	Cap-H2, CBP, Chro, fs(1)h, l(3)mbt, pzg, TfIIIC, vtd	Li L et al., Mol Cell. 2015
GSE80700	GAF, Ibf1, Ibf2, Nup98, pita, ZIPIC	Cubeñas-Potts C et al., Nucleic Acids Res. 2017

References

Yang J, Sung E, Donlin-Asp PG, Corces VG. A subset of Drosophila Myc sites remain associated with mitotic chromosomes colocalized with insulator proteins. Nat Commun. 2013;4:1464.

Gurudatta BV, Yang J, Van Bortle K, Donlin-Asp PG, Corces VG. Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle. Cell Cycle. 2013 May 15;12(10):1605-15.

Li L, Lyu X, Hou C, Takenaka N, Nguyen HQ, Ong CT, Cubeñas-Potts C, Hu M, Lei EP, Bosco G, Qin ZS, Corces VG. Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing. Mol Cell. 2015 Apr 16;58(2):216-31.

Cubeñas-Potts C, Rowley MJ, Lyu X, Li G, Lei EP, Corces VG. Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture. Nucleic Acids Res. 2017 Feb 28;45(4):1714-1730.

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.