Dataset BDTNP1_TFBS_Mad

General Information
Name	BDTNP1_TFBS_Mad	Species	D. melanogaster
Dataset type	genomic sequence feature	FlyBase ID	FBlc0000310
Source & Content
Consists of	Genomic sequences identified by ChIP-chip. (The modENCODE Consortium, 2010, MacArthur et al., 2009)
Created by
Available from	Not available as reagents.
Strain
Stage & tissue
Stage Tissue/Position (including subcellular localization) Reference embryonic stage 5 (MacArthur et al., 2009) Comment:2.5-3.5 hr AEL, correspondence to mid- and late embryonic stage 5 specified by authors.
Cell Line
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Description & Members
Description	Genomic sequences identified as Mad transcription factor binding sites; chromatin immunoprecipitation using an antibody against the Mad protein; DNA sequences identified by genomic tiling array. (The modENCODE Consortium, 2010, MacArthur et al., 2009)
Parent collections	mE1_TFBS_HSA
Component collection(s)
Number in collection
Comment on number in collection
Members
Experimental protocol
Vector
Sample preparation	Chromatin was prepared as previously described (FBrf0205197). Wild-type embryos from 2.5 hr to 3.5 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. (MacArthur et al., 2009)
Collection preparation	Pre-cleared chromatin was incubated with affinity-purified polyclonal antibody directed against Mad 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). (MacArthur et al., 2009)
Mode of assay	ChIP-chip (MacArthur et al., 2009)
Assay platform	Affymetrix Drosophila Melanogaster Antisense Tiling Array (MacArthur et al., 2009)
Data analysis	Data analysis was as previously described (FBrf0205197). 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. (MacArthur et al., 2009) Data was re-mapped to the April 2006 assembly of the D. melanogaster genome (dm3, BDGP release 5). (Ma, 2011.6.8)
Additional data
	More information is available under: GEO: GPL3923 UCSC: bdtnpMad2Fdr1
Associated files
Additional sites
Comments
	Original data generated by BDTNP (FBrf0208649). 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 bdtnpMad2Fdr1.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	BDTNP1_TFBS_Mad bdtnp_mad.gff (The modENCODE Consortium, 2010, Ma, 2011.6.8) MAD bound regions (MacArthur et al., 2009)
Secondary FlyBase IDs

References ( 3 )
Research paper	MacArthur et al., 2009, Genome Biol. 10(7): R80 Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. [FBrf0208649]
Supplementary material	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]