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

Database: dm6 Primary Table: CP190_interphase_macs Row Count: 12,458 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	47446	`int(10) unsigned`	range
`chromEnd`	47566	`int(10) unsigned`	range
`name`	CP190_interphase_macs_peak_1	`varchar(255)`	values
`score`	86	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	5.39967	`float`	range
`pValue`	10.4985	`float`	range
`qValue`	8.63561	`float`	range
`peak`	78	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	47446	47566	CP190_interphase_macs_peak_1	86	.	5.39967	10.4985	8.63561	78
585	chr2L	65659	66025	CP190_interphase_macs_peak_2	1764	.	41.0856	179.47	176.472	221
585	chr2L	66390	66519	CP190_interphase_macs_peak_3	77	.	5.11548	9.61767	7.77425	64
585	chr2L	66818	67065	CP190_interphase_macs_peak_4	89	.	4.11642	10.8146	8.94445	110
585	chr2L	71589	71812	CP190_interphase_macs_peak_5	209	.	8.49761	22.9755	20.9162	123
585	chr2L	72005	74006	CP190_interphase_macs_peak_6a	2476	.	42.1985	251.254	247.69	351
585	chr2L	72005	74006	CP190_interphase_macs_peak_6b	998	.	19.1553	102.425	99.8281	582
585	chr2L	72005	74006	CP190_interphase_macs_peak_6c	2449	.	25.0949	248.474	244.942	1295
585	chr2L	72005	74006	CP190_interphase_macs_peak_6d	784	.	15.4038	80.9214	78.4351	1829
585	chr2L	74250	74378	CP190_interphase_macs_peak_7	99	.	5.51067	11.8182	9.92646	68

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.