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

Database: dm6 Primary Table: GSE62904_Chro_peakzilla Row Count: 9,101 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	73097	`int(10) unsigned`	range
`chromEnd`	73521	`int(10) unsigned`	range
`name`	peakzilla_4583	`varchar(255)`	values
`score`	3	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.91	`float`	range
`pValue`	-1	`float`	range
`qValue`	1.38722	`float`	range
`peak`	212	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	73097	73521	peakzilla_4583	3	.	2.91	-1	1.38722	212
585	chr2L	88385	88809	peakzilla_7044	2	.	2.5	-1	0.74088	212
585	chr2L	94561	94985	peakzilla_4072	4	.	4.76	-1	1.82974	212
585	chr2L	99522	99946	peakzilla_15990	1	.	2.29	-1	0.40882	212
585	chr2L	102098	102522	peakzilla_1221	14	.	13.26	-1	2.60206	212
585	chr2L	106542	106966	peakzilla_3840	4	.	4.01	-1	1.92812	212
585	chr2L	107659	108083	peakzilla_2826	7	.	10.79	-1	2.25181	212
585	chr2L	114425	114849	peakzilla_2608	8	.	7.4	-1	2.37675	212
586	chr2L	140099	140523	peakzilla_5510	2	.	2.72	-1	1.00922	212
586	chr2L	143042	143466	peakzilla_2868	7	.	9.07	-1	2.25964	212

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.