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

Database: dm6 Primary Table: GSE62904_CapH2_macs Row Count: 5,898 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	72094	`int(10) unsigned`	range
`chromEnd`	72359	`int(10) unsigned`	range
`name`	GSE62904_CapH2_macs_peak_1	`varchar(255)`	values
`score`	53	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	2.68413	`float`	range
`pValue`	7.08715	`float`	range
`qValue`	5.32436	`float`	range
`peak`	109	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	72094	72359	GSE62904_CapH2_macs_peak_1	53	.	2.68413	7.08715	5.32436	109
585	chr2L	72558	72786	GSE62904_CapH2_macs_peak_2	67	.	2.92096	8.5709	6.78471	94
585	chr2L	73100	73677	GSE62904_CapH2_macs_peak_3	323	.	5.92087	34.3673	32.3529	235
585	chr2L	94569	94970	GSE62904_CapH2_macs_peak_4	295	.	4.89534	31.5938	29.5994	165
585	chr2L	102044	102644	GSE62904_CapH2_macs_peak_5	4491	.	30.4763	452.281	449.133	284
585	chr2L	106567	106895	GSE62904_CapH2_macs_peak_6	144	.	3.94265	16.3428	14.467	184
585	chr2L	107149	108138	GSE62904_CapH2_macs_peak_7a	31	.	2.2894	4.86285	3.14608	54
585	chr2L	107149	108138	GSE62904_CapH2_macs_peak_7b	944	.	11.0523	96.784	94.4857	738
585	chr2L	109155	109353	GSE62904_CapH2_macs_peak_8	31	.	2.2894	4.86285	3.14608	130
585	chr2L	114424	114868	GSE62904_CapH2_macs_peak_9	1396	.	13.175	142.066	139.623	206

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.