FB2026_03 , released September 17, 2026
Result: mE1_TFBS_cad
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General Information
Name
mE1_TFBS_cad
Species
D. melanogaster
Result type
binding site identification
FlyBase ID
FBlc0000288
Project
Data Provider
Title
cad binding sites (peak calls) identified by ChIP-chip and ChIP-Seq in embryos.
Status
Current
Accessions
    Biosample Source
    Overview
    Strain
    iso-1
    (Negre et al., 2011)
    Stage
    pre-blastoderm stage
    (Negre et al., 2011)
    blastoderm stage
    (Negre et al., 2011)
    gastrula stage
    (Negre et al., 2011)
    early extended germ band stage
    (Negre et al., 2011)
    late extended germ band stage
    (Negre et al., 2011)
    Sex
    Tissue isolated
    organism
    (Negre et al., 2011)
    Other tissues studied
    Cell component
    Cell line
    Key genes
    (transgene_used)
    Methods
    Sample preparation
    Biosamples analyzed by this result (5)
    Biosample
    Type
    Title
    BS_mE2570
    whole organism
    D. melanogaster, iso-1 strain, embryo (0-4 hr AEL), source for ChIP.
    BS_mE2578
    whole organism
    D. melanogaster, cad-GFP, embryo (4-8 hr AEL), source for ChIP.
    BS_mE2626
    whole organism
    D. melanogaster, cad-GFP, embryo (0-4 hr AEL), source for ChIP.
    BS_mE2637
    whole organism
    D. melanogaster, cad-GFP, embryo (4-8 hr AEL), source for ChIP.
    BS_mE902
    whole organism
    D. melanogaster, cad-GFP, embryo (0-4 hr AEL), source for ChIP.
    Data Analyzed
    Assay
    ChIP-Seq
    (Negre et al., 2011)
    ChIP-chip
    (Negre et al., 2011)
    Assay methods
    single-end layout
    (Negre et al., 2011)
    Illumina sequencing
    (Negre et al., 2011)
    Key genes
    (bait_protein)
    Protocol
    Mode of Assay
    Raw Data Analyzed (5)
    Assay / Reagent collection
    Type
    Title
    ChIP-chip_mE902_cad_E1-9
    ChIP-chip
    ChIP-chip of cad in D. melanogaster, cad-GFP, embryo (0-4 hr AEL).
    ChIP-chip_mE2570_cad_E1-9
    ChIP-chip
    ChIP-chip of cad in D. melanogaster, iso-1 strain, embryo (0-4 hr AEL).
    ChIP-chip_mE2578_cad_E9-12
    ChIP-chip
    ChIP-chip of cad in D. melanogaster, cad-GFP, embryo (4-8 hr AEL).
    ChIP-Seq_mE2626_cad_E1-9
    ChIP-Seq
    ChIP-Seq of cad in D. melanogaster, cad-GFP, embryo (0-4 hr AEL).
    ChIP-Seq_mE2637_cad_E9-12
    ChIP-Seq
    ChIP-Seq of cad in D. melanogaster, cad-GFP, embryo (4-8 hr AEL).
    Processed Data Analyzed (0)
    Result
    Type
    Title
    Analysis
    Methods
    Reference Genome
    Reference Annotation
    Data analysis

    Peaks from multiple embryonic ChIP data sets were merged and the union was taken.

    (Nègre et al., 2011)
    Comments

    The related GFF3 file in Data S7 of the modENCODE integrative fly paper (FBrf0213603) corresponds to the union of modENCODE_902, modENCODE_2570, modENCODE_2578, modENCODE_2626 and modENCODE_2637. For the modENCODE_2570 and modENCODE_2578 ChIP data sets, an older peak calling analysis was used; the peak calls used here differ from the updated modENCODE versions, 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)
    Associated Data
    Size
    Associated features
    8,701 TF_binding_site(s)
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    Files
    Additional Information
    Synonyms and Secondary IDs (4)
    Reported As
    Symbol Synonym
    Embryo_cad.gff
    (Ma, 2011.6.8, The modENCODE Consortium, 2010)
    cad TFBS
    (Negre et al., 2011)
    mE1_TFBS_cad
    (Schroeder, 2014.6.12)
    Name Synonyms
    cad binding sites (peak calls) identified by ChIP-chip and ChIP-Seq in embryos.
    (Nègre et al., 2011)
    Secondary FlyBase IDs
      References (6)