Schema for Architectural Proteins ChIP-Seq (Kc167) - ChIP-Seq of Architectural Proteins in Kc167 Cells
  Database: dm6    Primary Table: BEAF_mitosis_macs    Row Count: 3,199   Data last updated: 2020-08-21
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom chr2Lvarchar(255) values
chromStart 72585int(10) unsigned range
chromEnd 72747int(10) unsigned range
name BEAF_mitosis_macs_peak_1varchar(255) values
score 27int(10) unsigned range
strand .char(1) values
signalValue 3.24284float range
pValue 4.98373float range
qValue 2.75381float range
peak 99int(11) range

Sample Rows
 
binchromchromStartchromEndnamescorestrandsignalValuepValueqValuepeak
585chr2L7258572747BEAF_mitosis_macs_peak_127.3.242844.983732.7538199
585chr2L7329373468BEAF_mitosis_macs_peak_2135.4.2002916.056713.529663
585chr2L9465994803BEAF_mitosis_macs_peak_398.5.9612712.3129.848178
585chr2L102163102683BEAF_mitosis_macs_peak_42157.33.7455219.828215.704166
585chr2L102774102919BEAF_mitosis_macs_peak_530.3.387445.257753.00771102
585chr2L114509114770BEAF_mitosis_macs_peak_6927.17.784695.967492.7544120
586chr2L143217143437BEAF_mitosis_macs_peak_7377.12.193140.557237.7542107
586chr2L182711182917BEAF_mitosis_macs_peak_8189.8.3083921.535718.9338103
586chr2L203654203984BEAF_mitosis_macs_peak_9424.14.107245.287442.444299
586chr2L224265224609BEAF_mitosis_macs_peak_10285.11.190431.312628.6173

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.