Dataset BDTNP1_TFBS_bcd

General Information
Name	BDTNP1_TFBS_bcd	Species	D. melanogaster
Dataset type	genomic sequence feature	FlyBase ID	FBlc0000287
Source & Content
Consists of	Genomic sequences identified by ChIP-chip. (Li et al., 2008, The modENCODE Consortium, 2010)
Created by
Available from	Not available as reagents.
Strain
Stage & tissue
Stage Tissue/Position (including subcellular localization) Reference embryonic stage 4 -- 5 (Li et al., 2008) Comment:2-3 hr AEL, correspondence to late embryonic stage 4 and early embryonic stage 5 specified by authors.
Cell Line
Recent Updates
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FB2013_03
FB2013_02
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Description & Members
Description	Genomic sequences identified as bcd transcription factor binding sites; chromatin immunoprecipitation using an antibody against the bcd protein; DNA sequences identified by genomic tiling array. (Li et al., 2008, 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	Wild-type embryos from 2 hr to 3 hr of age were cross-linked in 5% formaldehyde saturated hexanes for 5 minutes then frozen. Cross-linked material was homogenized, lysed, and chromatin was purified by CsCl gradient before sonication to an average size of approximately 750bp. (Li et al., 2008)
Collection preparation	Pre-cleared chromatin was incubated with affinity-purified polyclonal antibody directed against bcd protein; two different antibody preparations were used, obtained by affinity-purification using non-overlapping portions of the bcd protein. Bound-chromatin was immunoprecipitated with protein-A beads. DNA from duplicate input chromatin samples, duplicate TF immunoprecipitations and duplicate control immunoprecipitations (normal rabbit IgG) was reverse cross-linked, purified and amplified using a random-prime-based PCR amplification protocol. Amplified DNA was fragmented with DNase I and biotinylated for microarray hybridization (in triplicate). (Li et al., 2008)
Mode of assay	ChIP-chip (Li et al., 2008)
Assay platform	Affymetrix Drosophila Melanogaster Antisense Tiling Array (Li et al., 2008)
Data analysis	ChIP-chip array data were processed using TiMAT. Only data for oligos mapping uniquely to release 4 of the D. melanogaster genome were considered. The mean hybridization intensity at each probe was divided by the mean probe intensity in the input DNA samples (three technical replicates). The logarithms of the ratios (IP/input) were averaged in 675-bp windows advanced one oligo at a time (lowest and highest values were dropped to produce a trimmed mean). Bound regions were identified by comparing the distribution of observed window scores to the computed symmetric null distribution: see Figure 1F in Li et al. (FBrf0205197). This estimated null distribution was used to assign p-values to each window, and a score threshold was chosen at 1%FDR. Bound regions ("intervals") were calculated from contiguous stretches of windows having scores above the given FDR threshold, requiring these contiguous stretches to contain at least ten windows with a maximum allowable gap of 200bp between any two adjacent windows. (Li et al., 2008) Data was re-mapped to the April 2006 assembly of the D. melanogaster genome (dm3, BDGP release 5). (Ma, 2011.6.8) 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: GPL3923 UCSC: bdtnpBcd1Fdr1 UCSC: bdtnpBcd2Fdr1
Associated files
Additional sites
Comments
	Original data generated by BDTNP (FBrf0205197). Data obtained by modENCODE group from http://hgdownload.cse.ucsc.edu/goldenPath/dm3/database/. The GFF3 file in Data S7 of the modENCODE integrative fly paper (FBrf0213603) corresponds to the union of bdtnpBcd1Fdr1.txt.gz and bdtnpBcd2Fdr1.txt.gz. (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	BCD bound regions (Li et al., 2008) bcd TFBS (Negre et al., 2011) BDTNP1_TFBS_bcd bdtnp_bcd.gff (The modENCODE Consortium, 2010, Ma, 2011.6.8)
Secondary FlyBase IDs

References ( 4 )
Research paper	Li et al., 2008, PLoS Biol. 6(2): e27 Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. [FBrf0205197]
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]