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

Database: dm6 Primary Table: GSE62904_fs1h_macs Row Count: 36,174 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	72509	`int(10) unsigned`	range
`chromEnd`	73871	`int(10) unsigned`	range
`name`	GSE62904_fs1h_macs_peak_1b	`varchar(255)`	values
`score`	443	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	5.2224	`float`	range
`pValue`	47.613	`float`	range
`qValue`	44.3938	`float`	range
`peak`	849	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	72509	73871	GSE62904_fs1h_macs_peak_1b	443	.	5.2224	47.613	44.3938	849
585	chr2L	72509	73871	GSE62904_fs1h_macs_peak_1a	196	.	3.58231	22.3941	19.6382	253
585	chr2L	72509	73871	GSE62904_fs1h_macs_peak_1c	21	.	1.72641	3.38385	2.18133	1251
585	chr2L	78893	79200	GSE62904_fs1h_macs_peak_2	47	.	1.9212	6.3223	4.70815	64
585	chr2L	81140	81298	GSE62904_fs1h_macs_peak_3	68	.	2.03108	8.78456	6.88924	74
585	chr2L	83369	83549	GSE62904_fs1h_macs_peak_4	22	.	1.5793	3.42446	2.21696	68
585	chr2L	83782	83978	GSE62904_fs1h_macs_peak_5	33	.	1.78119	4.73945	3.34087	137
585	chr2L	86439	86732	GSE62904_fs1h_macs_peak_6	85	.	2.30883	10.6013	8.52238	121
585	chr2L	91581	91904	GSE62904_fs1h_macs_peak_7	163	.	2.6631	18.9208	16.3041	170
585	chr2L	98657	98848	GSE62904_fs1h_macs_peak_8	28	.	1.66978	4.19033	2.87408	100

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.