Schema for Architectural Proteins ChIP-Seq (S2) - ChIP-Seq of Architectural Proteins in S2 Cells
  Database: dm6    Primary Table: GSE54337_Pita_peakzilla    Row Count: 6,458   Data last updated: 2020-08-21
fieldexampleSQL type info
bin 585smallint(5) unsigned range
chrom chr2Lvarchar(255) values
chromStart 34120int(10) unsigned range
chromEnd 34318int(10) unsigned range
name peakzilla_2134varchar(255) values
score 5int(10) unsigned range
strand .char(1) values
signalValue 5.33float range
pValue -1float range
qValue 3.30103float range
peak 99int(11) range

Sample Rows
 
binchromchromStartchromEndnamescorestrandsignalValuepValueqValuepeak
585chr2L3412034318peakzilla_21345.5.33-13.3010399
585chr2L3551035708peakzilla_73937.46.53-1309.65399
585chr2L3583836036peakzilla_46662.2.76-11.4122999
585chr2L4729947497peakzilla_103320.11.96-1399
585chr2L7228172479peakzilla_47602.3.01-11.3726399
585chr2L7251572713peakzilla_28753.2.91-12.8538799
585chr2L7309673294peakzilla_47580.65.57-1309.65399
585chr2L7379273990peakzilla_58258.51.02-1309.65399
585chr2L102214102412peakzilla_51172.44.9-1309.65399
585chr2L106152106350peakzilla_59782.2.2-10.9122299

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Architectural Proteins ChIP-Seq (S2) (insulatorsS2ChIPSeq) Track Description
 

Description

These tracks show the results of the ChIP-Seq analyses of architectural proteins (also known as insulators) from S2 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
GSE46614Cp190, Ibf1, Ibf2Cuartero S et al., EMBO J. 2014
GSE54337pita, ZIPICMaksimenko O et al., Genome Res. 2015

References

Maksimenko O, Bartkuhn M, Stakhov V, Herold M, Zolotarev N, Jox T, Buxa MK, Kirsch R, Bonchuk A, Fedotova A, Kyrchanova O, Renkawitz R, Georgiev P. Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin. Genome Res. 2015 Jan;25(1):89-99.

Cuartero S, Fresán U, Reina O, Planet E, Espinàs ML. Ibf1 and Ibf2 are novel CP190-interacting proteins required for insulator function. EMBO J. 2014 Mar 18;33(6):637-47.

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.