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

Database: dm6 Primary Table: GSE62904_CBP_macs Row Count: 16,407 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	66338	`int(10) unsigned`	range
`chromEnd`	67428	`int(10) unsigned`	range
`name`	GSE62904_CBP_macs_peak_1a	`varchar(255)`	values
`score`	143	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.54728	`float`	range
`pValue`	15.7956	`float`	range
`qValue`	14.3226	`float`	range
`peak`	131	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	66338	67428	GSE62904_CBP_macs_peak_1a	143	.	2.54728	15.7956	14.3226	131
585	chr2L	66338	67428	GSE62904_CBP_macs_peak_1b	1074	.	6.32924	109.469	107.45	580
585	chr2L	72109	74460	GSE62904_CBP_macs_peak_2a	169	.	2.70164	18.4039	16.9031	257
585	chr2L	72109	74460	GSE62904_CBP_macs_peak_2b	369	.	3.73075	38.6469	36.9813	521
585	chr2L	72109	74460	GSE62904_CBP_macs_peak_2c	2197	.	9.54519	222.073	219.718	1123
585	chr2L	72109	74460	GSE62904_CBP_macs_peak_2d	196	.	2.88174	21.16	19.6286	1796
585	chr2L	72109	74460	GSE62904_CBP_macs_peak_2e	210	.	2.95892	22.591	21.0467	2225
585	chr2L	85776	86217	GSE62904_CBP_macs_peak_3	448	.	3.80986	46.53	44.8147	234
585	chr2L	87242	87798	GSE62904_CBP_macs_peak_4	170	.	2.58155	18.5913	17.0901	192
585	chr2L	88302	88787	GSE62904_CBP_macs_peak_5	490	.	3.93476	50.822	49.0837	277

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.