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General Information
Symbol
Dmel\TFBS_da_008984
Species
D. melanogaster
Feature type
FlyBase ID
FBsf0000329868
Collection
Associated gene
Genomic Location
Chromosome (arm)
3R
Sequence location

3R:19,994,537..19,995,557

Sequence Data
Length
1021
Comments
Associated Information
Gene(s) (targeted or local)
    Allele(s)
      Transcripts(s)
        Polypeptide(s)
          Construct
            Experimental Data
            Binding data
            Bound moiety
            da protein
            Comments on moiety
            Mapped to restriction fragment
            Evidence or Assay
            Collection Information
            Collection: BDTNP1_TFBS_da
            Title
            ChIP-chip peak calls for da in D. melanogaster, embryo (stage 4-5).
            Source and Progenitors
            Species of derivation
            D. melanogaster
            Strain of derivation
            Stage
            Tissue/Position (including subcellular localization)
            Reference
            Vector of progenitor construct
            Description

            Genomic sequences identified as da transcription factor binding sites; chromatin immunoprecipitation using an antibody against the da protein; DNA sequences identified by genomic tiling array.

            Additional data
            Sample preparation

            Embryos were collected aged appropriately, then dechorionated and formaldehyde fixed. Fixed embryos were then homogenized, nuclei were pelleted, and chromatin was sheared by sonication.

            Collection preparation

            Chromatin was immunoprecipitated using the appropriate antibody and the recovered material was amplified by PCR.

            Mode of assay

            The recovered material was characterized by Affymetrix whole-genome tiling array.

            Data analysis

            Data analysis was as described elsewhere (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.

            Cell lines
            Observed in
            Not observed in
            Comments
            Stocks (0)
            External Crossreferences and Linkouts ( 0 )
            Synonyms and Secondary IDs (1)
            Reported As
            Symbol Synonym
            TFBS_da_008984
            Secondary FlyBase IDs
              References (2)