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

Database: dm6 Primary Table: GSE62904_TFIIIC_macs Row Count: 6,849 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	66852	`int(10) unsigned`	range
`chromEnd`	67027	`int(10) unsigned`	range
`name`	GSE62904_TFIIIC_macs_peak_1	`varchar(255)`	values
`score`	92	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.56766	`float`	range
`pValue`	11.6163	`float`	range
`qValue`	9.2986	`float`	range
`peak`	87	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	66852	67027	GSE62904_TFIIIC_macs_peak_1	92	.	3.56766	11.6163	9.2986	87
585	chr2L	71534	72759	GSE62904_TFIIIC_macs_peak_2a	359	.	6.86088	38.8709	35.9835	153
585	chr2L	71534	72759	GSE62904_TFIIIC_macs_peak_2b	515	.	8.41602	54.6335	51.5662	628
585	chr2L	71534	72759	GSE62904_TFIIIC_macs_peak_2c	149	.	4.39097	17.4525	14.9544	1059
585	chr2L	72960	73822	GSE62904_TFIIIC_macs_peak_3	2705	.	24.6077	274.492	270.563	345
585	chr2L	87349	87793	GSE62904_TFIIIC_macs_peak_4a	184	.	4.31366	21.073	18.4876	117
585	chr2L	87349	87793	GSE62904_TFIIIC_macs_peak_4b	93	.	3.2192	11.688	9.36955	337
585	chr2L	102183	102605	GSE62904_TFIIIC_macs_peak_5	497	.	8.02866	52.7924	49.7446	158
585	chr2L	107838	108314	GSE62904_TFIIIC_macs_peak_6	213	.	5.21427	24.0098	21.3618	244
585	chr2L	114558	114715	GSE62904_TFIIIC_macs_peak_7	41	.	2.55994	6.14141	4.10591	76

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.