General Information
Name
mE1_HDAC_PRE
Species
D. melanogaster
Result type
FlyBase ID
FBlc0000414
Project
Data Provider
Title
Putative polycomb silencers identified by ChIP-chip of HDAC and histone modifications in embryos.
Status
Current
Accessions
    Biosample Source
    Overview
    Sex
    Tissue isolated
    Other tissues studied
    Cell component
    Cell line
    Key genes
    Methods
    Sample preparation
    Biosamples analyzed by this result (6)
    Biosample
    Type
    Title
    D. melanogaster, iso-1 strain, embryo (0-12 hr AEL), source for ChIP.
    D. melanogaster, iso-1 strain, embryo (0-12 hr AEL), source for ChIP.
    D. melanogaster, iso-1 strain, embryo (0-12 hr AEL), source for ChIP.
    D. melanogaster, iso-1 strain, embryo (0-12 hr AEL), source for ChIP.
    D. melanogaster, iso-1 strain, embryo (0-12 hr AEL), source for ChIP.
    D. melanogaster, iso-1 strain, embryo (0-12 hr AEL), source for ChIP.
    Data Analyzed
    Assay methods
    Key genes
    (bait_protein)
    Protocol
    Mode of Assay
    Raw Data Analyzed (6)
    Assay / Reagent collection
    Type
    Title
    ChIP-chip of H3K4me3 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL).
    ChIP-chip of H3K27me3 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL).
    ChIP-chip of HDAC1 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL).
    ChIP-chip of HDAC1 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL).
    ChIP-chip of HDAC4 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL).
    ChIP-chip of HDAC4 in D. melanogaster, iso-1 strain, embryo (0-12 hr AEL).
    Processed Data Analyzed (0)
    Result
    Type
    Title
    Analysis
    Methods
    Reference Genome
    Reference Annotation
    Data analysis
    Peak calling for ChIP-chip experiments was performed using MAT (Johnson et al. 2006. Proc. Natl. Acad. Sci. U.S.A. 103(33): 12457-12462.). The union of Rpd3 (HDAC1) and HDAC4 peaks was filtered to remove those regions that overlap the His3 modification H3K4me3. The remaining HDAC1/HDAC4 sites that overlapped regions of H3K27me3 modification were taken to generate a list of 537 predicted silencers.
    Comments
    Associated Data
    Size
    Associated features
    537 silencer(s)
    Files
    Additional Information
    Synonyms and Secondary IDs (7)
    Reported As
    Symbol Synonym
    HDAC associated PREs
    Prediction of silencers
    mE1_HDAC_PRE
    putative PREs
    Name Synonyms
    Putative polycomb silencers identified by ChIP-chip of HDAC and histone modifications in embryos.
    Secondary FlyBase IDs
      References (4)