Basal Transcription Factors ChIP-Seq Track Settings
 
Basal Transcription Factors ChIP-Seq   (All ChIP Seq Tracks)

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 M1BP Peaks  M1BP Peaks for S2R+ Cells   Schema 
 
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 M1BP logLR  M1BP Log Likelihood Enrichment for S2R+ Cells   Schema 
 
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 GAF Peaks  GAF Peaks for S2-DRSC Cells   Schema 
 
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 GAF logLR  GAF Log Likelihood Enrichment for S2-DRSC Cells   Schema 
 
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 GAF-KD GAF Peaks  GAF-KD GAF Peaks for S2-DRSC Cells   Schema 
 
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 GAF-KD GAF logLR  GAF-KD GAF Log Likelihood Enrichment for S2-DRSC Cells   Schema 
 
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 GAF Peaks for Embryos  GAF Peaks for Drosophila 8-16h Embryos   Schema 
 
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 GAF logLR for Embryos  GAF Log Likelihood Enrichment for Drosophila 8-16h Embryos   Schema 
 
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 GAF Peaks for Embryos (modENCODE)  GAF Peaks for Drosophila 8-16h Embryos (modENCODE)   Schema 
 
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 GAF logLR for Embryos (modENCODE)  GAF Log Likelihood Enrichment for Drosophila 8-16h Embryos (modENCODE)   Schema 
 
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 TBP Ab517 Peaks  TBP Peaks (Antibody 517) for Drosophila 2-4h Embryos   Schema 
 
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 TBP Ab517 logLR  TBP (Antibody 517) Log Likelihood Enrichment for Drosophila 2-4h Embryos   Schema 
 
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 TBP Ab518 Peaks  TBP Peaks (Antibody 517) for Drosophila 2-4h Embryos   Schema 
 
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 TBP Ab518 logLR  TBP (Antibody 518) Log Likelihood Enrichment for Drosophila 2-4h Embryos   Schema 
 
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 TRF2 Ab274 Peaks  TRF2 Peaks (Antibody 274) for Drosophila 2-4h Embryos   Schema 
 
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 TRF2 Ab274 logLR  TRF2 (Antibody 274) Log Likelihood Enrichment for Drosophila 2-4h Embryos   Schema 
 
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 TRF2 Ab275 Peaks  TRF2 Peaks (Antibody 275) for Drosophila 2-4h Embryos   Schema 
 
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 TRF2 Ab275 logLR  TRF2 (Antibody 275) Log Likelihood Enrichment for Drosophila 2-4h Embryos   Schema 
    

Description

These tracks show the results of the ChIP-Seq analyses of transcription factors that are associated with the core promoter. The peak calls and the log likelihood ratio evidence tracks were produced by MACS.

The ChIP-Seq datasets were obtained from the Gene Expression Omnibus database at NCBI under the following accession numbers:

AccessionTranscription FactorsReference
GSE46630M1BPLi J and Gilmour DS, EMBO J. 2013
GSE40646GAF, GAF-KDFuda NJ et al., PLoS Genet. 2015
GSE38594GAF (Embryos)Oh H et al., Cell Rep. 2013
GSE50374GAF (Embryos; modENCODE)modENCODE
GSE52029TBP, TRF2Wang YL et al., Genes Dev. 2014

Credits

Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT. GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters. PLoS Genet. 2015 Mar 27;11(3):e1005108.

Oh H, Slattery M, Ma L, Crofts A, White KP, Mann RS, Irvine KD. Genome-wide association of Yorkie with chromatin and chromatin-remodeling complexes. Cell Rep. 2013 Feb 21;3(2):309-18.

Landt SG, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep;22(9):1813-31.

Li J, Gilmour DS. Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor. EMBO J. 2013 Jul 3;32(13):1829-41.

Wang YL, Duttke SH, Chen K, Johnston J, Kassavetis GA, Zeitlinger J, Kadonaga JT. TRF2, but not TBP, mediates the transcription of ribosomal protein genes. Genes Dev. 2014 Jul 15;28(14):1550-5.

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.