Schema for Architectural Proteins ChIP-Seq (Kc167) - ChIP-Seq of Architectural Proteins in Kc167 Cells
  Database: dm6    Primary Table: GSE80700_GAF_macs    Row Count: 11,124   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom chr2Lvarchar(255) values
chromStart 66337int(10) unsigned range
chromEnd 67536int(10) unsigned range
name GSE80700_GAF_macs_peak_1bvarchar(255) values
score 39449int(10) unsigned range
strand .char(1) values
signalValue 194.365float range
pValue 3948.18float range
qValue 3944.93float range
peak 609int(11) range

Sample Rows
 
binchromchromStartchromEndnamescorestrandsignalValuepValueqValuepeak
585chr2L6633767536GSE80700_GAF_macs_peak_1b39449.194.3653948.183944.93609
585chr2L6633767536GSE80700_GAF_macs_peak_1c9764.64.2584979.008976.453981
585chr2L6633767536GSE80700_GAF_macs_peak_1a1996.20.11201.784199.622160
585chr2L7230973926GSE80700_GAF_macs_peak_2a22834.125.0562286.372283.47249
585chr2L7230973926GSE80700_GAF_macs_peak_2b914.11.972593.504791.4868788
585chr2L7230973926GSE80700_GAF_macs_peak_2c168.4.583218.567316.80111224
585chr2L7230973926GSE80700_GAF_macs_peak_2d449.7.7633846.882444.97821458
585chr2L107486109629GSE80700_GAF_macs_peak_3a108.3.7413912.549210.837888
585chr2L107486109629GSE80700_GAF_macs_peak_3b42614.206.9924264.784261.47592
585chr2L107486109629GSE80700_GAF_macs_peak_3c506.8.3245952.589550.6671220

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.