Dataset mE1_TFBS_D

General Information
Name	mE1_TFBS_D	Species	D. melanogaster
Dataset type	genomic sequence feature	FlyBase ID	FBlc0000291
Source & Content
Consists of	Genomic sequences identified by integrative analysis of several ChIP data sets. (The modENCODE Consortium, 2010)
Created by
Available from	Not available as reagents.
Strain	iso-1 (Ma, 2011.6.8)
Stage & tissue
Stage Tissue/Position (including subcellular localization) Reference embryonic stage 1 -- 15 (Negre et al., 2011) Comment:A combination of ChIP data sets derived from 0-8 hr AEL and 0-12 hr AEL embryos.
Cell Line
Recent Updates
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FB2013_03
FB2013_02
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Description & Members
Description	Genomic sequences identified as D transcription factor binding sites; chromatin immunoprecipitation using an antibody against the D protein; DNA sequences identified by genomic tiling array; an integrative analysis of multiple ChIP data sets. (The modENCODE Consortium, 2010)
Parent collections	mE1_TFBS_HSA
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 polyclonal antibodies raised against D protein. Different polyclonal antibodies to D were used in different ChIP experiments. 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	Peaks from multiple embryonic ChIP data sets were merged and the union was taken. (Negre et al., 2011)
Additional data
	More information is available under: GEO: GPL6629 GEO: GSM399633 GEO: GSM621330 modMine: modENCODE_626 modMine: modENCODE_2571
Associated files
Additional sites
Comments
	The related GFF3 file in Data S7 of the modENCODE integrative fly paper (FBrf0213603) corresponds to the union of modENCODE_626 and modENCODE_2571. For modENCODE_2571, an older peak calling analysis was used; the peak calls used here differ from the updated modENCODE version, though the underlying raw data are the same. (Ma, 2011.6.8) This data set was one of 41 TF data sets used by the modENCODE consortium in an integrative "HOT spot analysis" (see Parent Collection FBlc0000258 for more details). (Ma, 2011.6.8)
Synonyms & Secondary IDs
Reported As
Symbol Synonym	D TFBS (Negre et al., 2011) Embryo_D.gff (The modENCODE Consortium, 2010, Ma, 2011.6.8) mE1_TFBS_D
Secondary FlyBase IDs

References ( 3 )
Supplementary material	Negre et al., 2011, Nature 471(7339): Supplementary Information. [FBrf0213507] The modENCODE Consortium, 2010, Science 330(6012): DataS7: Predicted TFBS. [FBrf0213603]
Personal communication to FlyBase	Ma, 2011.6.8, HOT spots analysis (Data Set S8) and 41 TFBS GFF files (Data Set S7). HOT spots analysis (Data Set S8) and 41 TFBS GFF files (Data Set S7). [FBrf0213928]