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

Database: dm6 Primary Table: dCTCF_mitosis_macs Row Count: 3,372 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	102510	`int(10) unsigned`	range
`chromEnd`	102774	`int(10) unsigned`	range
`name`	dCTCF_mitosis_macs_peak_1	`varchar(255)`	values
`score`	67	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	5.07878	`float`	range
`pValue`	9.89157	`float`	range
`qValue`	6.79169	`float`	range
`peak`	58	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	102510	102774	dCTCF_mitosis_macs_peak_1	67	.	5.07878	9.89157	6.79169	58
585	chr2L	122406	122542	dCTCF_mitosis_macs_peak_2	42	.	3.46511	7.00623	4.28777	66
586	chr2L	143401	143604	dCTCF_mitosis_macs_peak_3	79	.	5.7606	11.1639	7.91827	115
586	chr2L	203856	203978	dCTCF_mitosis_macs_peak_4	50	.	4.67946	7.85796	5.01957	45
586	chr2L	204022	204140	dCTCF_mitosis_macs_peak_5	29	.	3.74604	5.44073	2.96985	44
586	chr2L	207528	207787	dCTCF_mitosis_macs_peak_6	33	.	3.60338	5.89489	3.35587	62
586	chr2L	249927	250049	dCTCF_mitosis_macs_peak_7	47	.	4.51895	7.57597	4.78188	38
586	chr2L	252135	252252	dCTCF_mitosis_macs_peak_8	65	.	5.09885	9.58682	6.52915	52
587	chr2L	273168	273562	dCTCF_mitosis_macs_peak_9a	53	.	4.9121	8.26128	5.3714	122
587	chr2L	273168	273562	dCTCF_mitosis_macs_peak_9b	84	.	6.11226	11.7972	8.4816	338

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.