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

Database: dm6 Primary Table: GSE80700_Ibf1_macs Row Count: 6,686 Data last updated: 2020-08-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	64562	`int(10) unsigned`	range
`chromEnd`	66528	`int(10) unsigned`	range
`name`	GSE80700_Ibf1_macs_peak_1a	`varchar(255)`	values
`score`	70126	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	192.124	`float`	range
`pValue`	7015.9	`float`	range
`qValue`	7012.64	`float`	range
`peak`	447	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	64562	66528	GSE80700_Ibf1_macs_peak_1a	70126	.	192.124	7015.9	7012.64	447
585	chr2L	64562	66528	GSE80700_Ibf1_macs_peak_1b	47789	.	140.987	4782.07	4778.97	1283
585	chr2L	66734	66937	GSE80700_Ibf1_macs_peak_2	80	.	2.66981	9.88227	8.09857	108
585	chr2L	71537	74717	GSE80700_Ibf1_macs_peak_3a	859	.	8.11212	88.1108	85.9237	194
585	chr2L	71537	74717	GSE80700_Ibf1_macs_peak_3b	68354	.	188.17	6838.64	6835.4	732
585	chr2L	71537	74717	GSE80700_Ibf1_macs_peak_3c	17943	.	65.359	1797.14	1794.32	1758
585	chr2L	71537	74717	GSE80700_Ibf1_macs_peak_3d	447	.	5.64768	46.8169	44.7499	2336
585	chr2L	71537	74717	GSE80700_Ibf1_macs_peak_3e	145	.	3.33727	16.468	14.5906	2828
585	chr2L	71537	74717	GSE80700_Ibf1_macs_peak_3f	162	.	3.49129	18.1534	16.2581	3028
585	chr2L	77986	78493	GSE80700_Ibf1_macs_peak_4	104	.	2.53606	12.2603	10.4393	272

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.