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

Database: dm6 Primary Table: GSE80700_Ibf2_macs Row Count: 5,372 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	64683	`int(10) unsigned`	range
`chromEnd`	66369	`int(10) unsigned`	range
`name`	GSE80700_Ibf2_macs_peak_1b	`varchar(255)`	values
`score`	19555	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	70.9971	`float`	range
`pValue`	1958.6	`float`	range
`qValue`	1955.52	`float`	range
`peak`	1160	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	64683	66369	GSE80700_Ibf2_macs_peak_1b	19555	.	70.9971	1958.6	1955.52	1160
585	chr2L	64683	66369	GSE80700_Ibf2_macs_peak_1a	26712	.	90.465	2674.46	2671.26	327
585	chr2L	71562	73966	GSE80700_Ibf2_macs_peak_2a	189	.	3.77812	21.0276	18.9433	182
585	chr2L	71562	73966	GSE80700_Ibf2_macs_peak_2b	28764	.	95.8698	2879.71	2876.48	709
585	chr2L	71562	73966	GSE80700_Ibf2_macs_peak_2c	7005	.	32.9011	703.293	700.505	1734
585	chr2L	71562	73966	GSE80700_Ibf2_macs_peak_2d	132	.	3.25338	15.2822	13.2589	2309
585	chr2L	74296	74721	GSE80700_Ibf2_macs_peak_3a	21	.	1.88906	3.89164	2.15897	95
585	chr2L	74296	74721	GSE80700_Ibf2_macs_peak_3b	60	.	2.46627	7.99039	6.09489	267
585	chr2L	78059	78414	GSE80700_Ibf2_macs_peak_4	21	.	1.79157	3.90397	2.17073	48
585	chr2L	82043	83119	GSE80700_Ibf2_macs_peak_5a	26	.	1.84148	4.38062	2.62284	59

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.