Schema for Architectural Proteins ChIP-Seq (Kc167) - ChIP-Seq of Architectural Proteins in Kc167 Cells
  Database: dm6    Primary Table: GSE80700_ZIPIC_peakzilla    Row Count: 10,546   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom chr2Lvarchar(255) values
chromStart 64802int(10) unsigned range
chromEnd 65198int(10) unsigned range
name peakzilla_9960varchar(255) values
score 1int(10) unsigned range
strand .char(1) values
signalValue 2.38float range
pValue -1float range
qValue 0.12274float range
peak 198int(11) range

Sample Rows
 
binchromchromStartchromEndnamescorestrandsignalValuepValueqValuepeak
585chr2L6480265198peakzilla_99601.2.38-10.12274198
585chr2L6567266068peakzilla_74962.4.26-10.26114198
585chr2L7210872504peakzilla_55044.8.8-11.29243198
585chr2L7308873484peakzilla_151015.13.16-12.00877198
585chr2L8589386289peakzilla_93201.2.55-10.12505198
585chr2L8716387559peakzilla_76442.3.16-10.23441198
585chr2L9454494940peakzilla_32078.7.49-12.11351198
585chr2L102147102543peakzilla_144015.17.38-11.98716198
585chr2L104834105230peakzilla_100281.2.29-10.12274198
585chr2L106587106983peakzilla_47765.4.19-11.73283198

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:

AccessionInsulatorsReference
GSE32584BEAF-32, Cp190, CTCFYang J et al., Nat Commun. 2013
GSE39521MycYang J et al., Nat Commun. 2013
GSE39664DrefGurudatta BV et al., Cell Cycle. 2013
GSE62904Cap-H2, CBP, Chro, fs(1)h, l(3)mbt, pzg, TfIIIC, vtdLi L et al., Mol Cell. 2015
GSE80700GAF, Ibf1, Ibf2, Nup98, pita, ZIPICCubeñas-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.