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

Database: dm6 Primary Table: BEAF_mitosis_macs Row Count: 3,199 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	72585	`int(10) unsigned`	range
`chromEnd`	72747	`int(10) unsigned`	range
`name`	BEAF_mitosis_macs_peak_1	`varchar(255)`	values
`score`	27	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.24284	`float`	range
`pValue`	4.98373	`float`	range
`qValue`	2.75381	`float`	range
`peak`	99	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	72585	72747	BEAF_mitosis_macs_peak_1	27	.	3.24284	4.98373	2.75381	99
585	chr2L	73293	73468	BEAF_mitosis_macs_peak_2	135	.	4.20029	16.0567	13.5296	63
585	chr2L	94659	94803	BEAF_mitosis_macs_peak_3	98	.	5.96127	12.312	9.8481	78
585	chr2L	102163	102683	BEAF_mitosis_macs_peak_4	2157	.	33.7455	219.828	215.704	166
585	chr2L	102774	102919	BEAF_mitosis_macs_peak_5	30	.	3.38744	5.25775	3.00771	102
585	chr2L	114509	114770	BEAF_mitosis_macs_peak_6	927	.	17.7846	95.9674	92.7544	120
586	chr2L	143217	143437	BEAF_mitosis_macs_peak_7	377	.	12.1931	40.5572	37.7542	107
586	chr2L	182711	182917	BEAF_mitosis_macs_peak_8	189	.	8.30839	21.5357	18.9338	103
586	chr2L	203654	203984	BEAF_mitosis_macs_peak_9	424	.	14.1072	45.2874	42.4442	99
586	chr2L	224265	224609	BEAF_mitosis_macs_peak_10	285	.	11.1904	31.3126	28.6	173

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.