Dataset mE1_CBP_Enhancers

General Information
Name	mE1_CBP_Enhancers	Species	D. melanogaster
Dataset type	genomic sequence feature	FlyBase ID	FBlc0000415
Source & Content
Consists of	Genomic sequences identified by ChIP-chip and ChIP-Seq. (Negre et al., 2011)
Created by
Available from	Not available as reagents.
Strain	iso-1 (Negre et al., 2011)
Stage & tissue
Stage Tissue/Position (including subcellular localization) Reference embryonic stage 1 -- 17 (Negre et al., 2011) Comment:0-24 hr AEL
Cell Line
Recent Updates
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FB2013_03
FB2013_02
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Description & Members
Description	Genomic sequences identified as putative embryo-only enhancers by virtue of embryo-specific CBP-binding in ChIP assays. A synthesis of ChIP-chip and ChIP-Seq data sets; DNA sequences identified by genomic tiling array or high-throughput sequencing. (Negre et al., 2011)
Parent collections
Component collection(s)
Number in collection
Comment on number in collection
Members
Experimental protocol
Vector
Sample preparation	Flies were cultivated in cages. Eggs were collected after a two hour pre-egg laying. Embryos of the desired age interval were collected and initially cross-linked in 1.8% formaldehyde for 15 minutes, then homogenized in buffered 1.8% formaladehyde and cross-linked for another 15 minutes. Cross-linked material was collected by centrifugation, washed, lysed and sonicated to an average size of 500bp. (Negre et al., 2011)
Collection preparation	Pre-cleared chromatin was incubated with antibodies specific to nej (CBP). Antibody-bound chromatin was immunoprecipitated with protein-A beads. Input and immunoprecipitated DNA was reverse-cross-linked, purified and processed for microarray hybridization or high-throughput sequencing. (Negre et al., 2011)
Mode of assay	ChIP-chip (Negre et al., 2011) ChIP-Seq (Negre et al., 2011)
Assay platform	Agilent-019182 Drosophila melanogaster Whole Genome ChIP-on-Chip Set 244K, Microarray 1 of 3 (Negre et al., 2011) Agilent-019183 Drosophila melanogaster Whole Genome ChIP-on-Chip Set 244K, Microarray 2 of 3 (Negre et al., 2011) Agilent-019184 Drosophila melanogaster Whole Genome ChIP-on-Chip Set 244K, Microarray 3 of 3 (Negre et al., 2011) Illumina Genome Analyzer (Negre et al., 2011)
Data analysis	Peak calling for ChIP-chip experiments was performed using MAT (Johnson et al. 2006. Proc. Natl. Acad. Sci. U.S.A. 103(33): 12457-12462). Peak calls from ChiP-Seq data were performed using MACS (Zhang et al. 2008. Genome Biol. 9(9): R137) or Peakseq (Rozowsky et al. 2009. Nat. Biotechnol. 27(1): 66-75). Peaks from CBP ChIP-chip and ChIP-seq experiments were filtered to exclude peaks falling between -500bp and +500bp of annotated promoters. CBP binding sites occuring at only one of the 12 developmental stages analyzed were also removed. Peaks were merged and a final list of sites occuring only during embryogenesis was generated. (Negre et al., 2011)
Additional data
	More information is available under: GEO: GPL6949 GEO: GPL6950 GEO: GPL6951 GEO: GPL9058 GEO: GSE15292 GEO: GSE15427 GEO: GSE16013 GEO: GSE23148 GEO: GSE25950 GEO: GSE25951 modMine: modENCODE_643 modMine: modENCODE_854 modMine: modENCODE_855 modMine: modENCODE_856 modMine: modENCODE_857 modMine: modENCODE_858 modMine: modENCODE_875 modMine: modENCODE_876 modMine: modENCODE_877 modMine: modENCODE_903 modMine: modENCODE_905
Associated files
Additional sites
Synonyms & Secondary IDs
Reported As
Symbol Synonym	CBP binding sites (Negre et al., 2011) CBP embryo only enhancer predictions (Negre et al., 2011, Negre et al., 2011) Embryo-specific CBP binding (Nègre et al., 2011) enhancers (Nègre et al., 2011) mE1_CBP_Enhancers
Secondary FlyBase IDs

References ( 3 )
Research paper	Nègre et al., 2011, Nature 471(7339): 527--531 A cis-regulatory map of the Drosophila genome. [FBrf0213303]
Supplementary material	Negre et al., 2011, Nature 471(7339): Supplementary Table 13 - CBP embryo only enhancer predictions. [FBrf0214517] Negre et al., 2011, Nature 471(7339): Supplementary Information. [FBrf0213507]