Schema for Architectural Proteins ChIP-Seq (Kc167) - ChIP-Seq of Architectural Proteins in Kc167 Cells
  Database: dm6    Primary Table: CP190_interphase_macs    Row Count: 12,458   Data last updated: 2020-08-21
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom chr2Lvarchar(255) values
chromStart 47446int(10) unsigned range
chromEnd 47566int(10) unsigned range
name CP190_interphase_macs_peak_1varchar(255) values
score 86int(10) unsigned range
strand .char(1) values
signalValue 5.39967float range
pValue 10.4985float range
qValue 8.63561float range
peak 78int(11) range

Sample Rows
 
binchromchromStartchromEndnamescorestrandsignalValuepValueqValuepeak
585chr2L4744647566CP190_interphase_macs_peak_186.5.3996710.49858.6356178
585chr2L6565966025CP190_interphase_macs_peak_21764.41.0856179.47176.472221
585chr2L6639066519CP190_interphase_macs_peak_377.5.115489.617677.7742564
585chr2L6681867065CP190_interphase_macs_peak_489.4.1164210.81468.94445110
585chr2L7158971812CP190_interphase_macs_peak_5209.8.4976122.975520.9162123
585chr2L7200574006CP190_interphase_macs_peak_6a2476.42.1985251.254247.69351
585chr2L7200574006CP190_interphase_macs_peak_6b998.19.1553102.42599.8281582
585chr2L7200574006CP190_interphase_macs_peak_6c2449.25.0949248.474244.9421295
585chr2L7200574006CP190_interphase_macs_peak_6d784.15.403880.921478.43511829
585chr2L7425074378CP190_interphase_macs_peak_799.5.5106711.81829.9264668

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.