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

Database: dm6 Primary Table: GSE62904_pzg_macs Row Count: 9,022 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	72064	`int(10) unsigned`	range
`chromEnd`	72299	`int(10) unsigned`	range
`name`	GSE62904_pzg_macs_peak_1	`varchar(255)`	values
`score`	107	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.33129	`float`	range
`pValue`	12.6649	`float`	range
`qValue`	10.7503	`float`	range
`peak`	100	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	72064	72299	GSE62904_pzg_macs_peak_1	107	.	3.33129	12.6649	10.7503	100
585	chr2L	72525	72861	GSE62904_pzg_macs_peak_2	154	.	3.88651	17.4256	15.4678	146
585	chr2L	73067	73877	GSE62904_pzg_macs_peak_3a	1045	.	10.8961	106.854	104.534	255
585	chr2L	73067	73877	GSE62904_pzg_macs_peak_3b	43	.	2.42907	6.1804	4.37361	591
585	chr2L	94603	94857	GSE62904_pzg_macs_peak_4	739	.	7.43839	76.1608	73.9307	123
585	chr2L	102129	102685	GSE62904_pzg_macs_peak_5	7310	.	39.4247	734.267	731.033	203
585	chr2L	103072	103439	GSE62904_pzg_macs_peak_6a	32	.	2.21785	5.0458	3.28979	51
585	chr2L	103072	103439	GSE62904_pzg_macs_peak_6b	38	.	2.32279	5.60192	3.82246	314
585	chr2L	106588	106890	GSE62904_pzg_macs_peak_7	709	.	8.60584	73.1556	70.9352	167
585	chr2L	107125	107424	GSE62904_pzg_macs_peak_8	86	.	3.05368	10.4908	8.60097	67

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.