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

Database: dm6 Primary Table: Myc_mitosis_macs Row Count: 4,181 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	65801	`int(10) unsigned`	range
`chromEnd`	65891	`int(10) unsigned`	range
`name`	Myc_mitosis_macs_peak_1	`varchar(255)`	values
`score`	22	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.6878	`float`	range
`pValue`	4.51036	`float`	range
`qValue`	2.27915	`float`	range
`peak`	27	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	65801	65891	Myc_mitosis_macs_peak_1	22	.	3.6878	4.51036	2.27915	27
585	chr2L	72194	72709	Myc_mitosis_macs_peak_2a	398	.	16.4776	43.0757	39.8105	95
585	chr2L	72194	72709	Myc_mitosis_macs_peak_2b	56	.	5.41754	8.15069	5.64157	364
585	chr2L	73062	73534	Myc_mitosis_macs_peak_3	970	.	16.7649	101.06	97.0417	195
585	chr2L	102176	102374	Myc_mitosis_macs_peak_4	110	.	7.74173	13.7199	11.0075	128
585	chr2L	114576	114746	Myc_mitosis_macs_peak_5	81	.	5.7581	10.7822	8.16361	77
585	chr2L	122359	122557	Myc_mitosis_macs_peak_6	166	.	8.61005	19.5115	16.6523	95
586	chr2L	131194	131355	Myc_mitosis_macs_peak_7	100	.	7.3756	12.7107	10.0289	94
586	chr2L	158861	159037	Myc_mitosis_macs_peak_8	112	.	7.12473	13.9923	11.27	92
586	chr2L	166656	166755	Myc_mitosis_macs_peak_9	36	.	4.2397	6.00354	3.62423	48

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.