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

Database: dm6 Primary Table: BEAF_interphase_peakzilla Row Count: 6,414 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	65757	`int(10) unsigned`	range
`chromEnd`	65961	`int(10) unsigned`	range
`name`	peakzilla_3540	`varchar(255)`	values
`score`	14	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	20.8	`float`	range
`pValue`	-1	`float`	range
`qValue`	2.85387	`float`	range
`peak`	102	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	65757	65961	peakzilla_3540	14	.	20.8	-1	2.85387	102
585	chr2L	72045	72249	peakzilla_3262	18	.	21.08	-1	3.04576	102
585	chr2L	72582	72786	peakzilla_4074	10	.	6.92	-1	2.56864	102
585	chr2L	73247	73451	peakzilla_970	148	.	61.19	-1	309.653	102
585	chr2L	94637	94841	peakzilla_2206	45	.	30.78	-1	309.653	102
585	chr2L	102232	102436	peakzilla_88	547	.	453.33	-1	309.653	102
585	chr2L	106642	106846	peakzilla_3966	10	.	15.23	-1	2.69897	102
585	chr2L	114515	114719	peakzilla_293	329	.	114.85	-1	309.653	102
585	chr2L	121042	121246	peakzilla_5389	4	.	2.38	-1	0.80244	102
586	chr2L	143213	143417	peakzilla_996	144	.	44.83	-1	309.653	102

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.