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General Information
Name
BDTNP1_TFBS_gt
Species
D. melanogaster
Result type
FlyBase ID
FBlc0000301
Project
Data Provider
Title
ChIP-chip peak calls for gt in D. melanogaster, embryo (stage 4-5).
Status
Current
Accessions
    Biosample Source
    Overview
    Strain
    Sex
    Tissue isolated
    Other tissues studied
    Cell component
    Cell line
    Key genes
    Methods
    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.
    Biosamples analyzed by this result (1)
    Biosample
    Type
    Title
    D. melanogaster, embryo (stage 4-5), source for chromatin (gt ChIP).
    Data Analyzed
    Assay methods
    Key genes
    (bait_protein)
    Protocol
    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.
    Raw Data Analyzed (1)
    Assay / Reagent collection
    Type
    Title
    ChIP-chip of gt in D. melanogaster, embryo (stage 4-5).
    Processed Data Analyzed (0)
    Result
    Type
    Title
    Analysis
    Methods
    Reference Genome
    Reference Annotation
    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.
    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 bdtnpGt2Fdr1.txt.gz.
    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).
    Associated Data
    Size
    Associated features
    2,094 TF_binding_site(s)
    Additional Information
    Synonyms and Secondary IDs (4)
    Reported As
    Symbol Synonym
    Name Synonyms
    ChIP-chip peak calls for gt in D. melanogaster, embryo (stage 4-5).
    Secondary FlyBase IDs
      References (5)