Dataset mE1_HDAC_PRE

General Information
Name	mE1_HDAC_PRE	Species	D. melanogaster
Dataset type	genomic sequence feature	FlyBase ID	FBlc0000414
Source & Content
Consists of	Genomic sequences identified by ChIP-chip. (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 -- 15 (Negre et al., 2011) Comment:0-12 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 polycomb response elements (silencers): regions of Rpd3 (HDAC1) or HDAC4 binding that overlap regions of His3 modification H3K27me3 but not H3K4me3. A synthesis of ChIP data sets; DNA sequences identified by genomic tiling array. (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	For each ChIP-chip experiment, pre-cleared chromatin was incubated with polyclonal antibodies specific to the target of interest. Two independent antibody preparations were used for ChIP of each HDAC. Commercial antibodies were used for ChIP of His3 modifications: Abcam, ab8580 (H3K4me3) and Upstate, 07-449 (H3K27me3). Antibody-bound chromatin was immunoprecipitated with protein-A beads. Input and immunoprecipitated DNA was reverse-cross-linked, purified, subjected to ligation mediated PCR for whole genome amplification and fluorescently labeled for microarray hybridization according to manufacturers' specifications. (Negre et al., 2011)
Mode of assay	ChIP-chip (Negre et al., 2011)
Assay platform	Affymetrix Drosophila Tiling 2.0R Array (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.). The union of Rpd3 (HDAC1) and HDAC4 peaks was filtered to remove those regions that overlap the His3 modification H3K4me3. The remaining HDAC1/HDAC4 sites that overlapped regions of H3K27me3 modification were taken to generate a list of 537 predicted silencers. (Negre et al., 2011)
Additional data
	More information is available under: GEO: GPL6629 GEO: GSE25956 GEO: GSE25957 GEO: GSE25960 GEO: GSE25961 GEO: GSM400362 GEO: GSM409076 modMine: modENCODE_622 modMine: modENCODE_919 modMine: modENCODE_2559 modMine: modENCODE_2560 modMine: modENCODE_2563 modMine: modENCODE_2564
Associated files
Additional sites
Synonyms & Secondary IDs
Reported As
Symbol Synonym	HDAC associated PREs (Negre et al., 2011) mE1_HDAC_PRE Prediction of silencers (Negre et al., 2011) PREs (Nègre et al., 2011) putative PREs (Negre et al., 2011) silencers (Nègre et al., 2011)
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 12 - HDAC associated PREs. [FBrf0214516] Negre et al., 2011, Nature 471(7339): Supplementary Information. [FBrf0213507]