Dataset mE1_TFBS_sbb

General Information
Name	mE1_TFBS_sbb	Species	D. melanogaster
Dataset type	genomic sequence feature	FlyBase ID	FBlc0000314
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 0-4 hr AEL and 0-12 hr AEL embryos.
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 sbb transcription factor binding sites; chromatin immunoprecipitation using an antibody against the sbb 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 antibody raised against sbb protein and 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: GSM400172 GEO: GSM621328 modMine: modENCODE_609 modMine: modENCODE_2569
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_609 and modENCODE_2569. For modENCODE_2569, 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	bks TFBS (Negre et al., 2011) Embryo_bks.gff (The modENCODE Consortium, 2010, Ma, 2011.6.8) mE1_TFBS_sbb
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]