FB2024_04 , released June 25, 2024
Result: ChIP-chip_tin_E2-4h_organism
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General Information
Name
ChIP-chip_tin_E2-4h_organism
Species
D. melanogaster
Result type
binding site identification
FlyBase ID
FBlc0000701
Project
Data Provider
[Furlong lab, EMBL](http://furlonglab.embl.de)
Title
ChIP-chip peak calls for tin from D. melanogaster, embyro (2-4 hr AEL).
Status
Current
Accessions
    Biosample Source
    Overview
    Strain
    Oregon-R
    (Zinzen et al., 2009)
    Stage
    blastoderm stage
    (Zinzen et al., 2009)
    gastrula stage
    (Zinzen et al., 2009)
    Sex
    Tissue isolated
    organism
    (Zinzen et al., 2009)
    Other tissues studied
    Cell component
    Cell line
    Key genes
    Methods
    Sample preparation
    Biosamples analyzed by this result (1)
    Biosample
    Type
    Title
    BS_Furlong_tin_E2-4h_organism
    whole organism
    D. melanogaster, embyro (2-4 hr AEL), source for chromatin.
    Data Analyzed
    Assay
    ChIP-chip
    (Zinzen et al., 2009)
    Assay methods
    Key genes
    (bait_protein)
    Protocol

    Two independent chromatin immunoprecipitations (ChIPs) were performed using two different anti-tin antibodies (FBrf0100308, FBrf0206680). These ChIPs were compared to two independent mock ChIPs using rabbit pre-immune sera, as previously described (FBrf0202481).

    Chromatin was prepared from formaldehyde-fixed embryos as previously described (FBrf0202481).

    Mode of Assay

    Immunoprecipitated chromatin was analyzed by Affymetrix GeneChip Drosophila Tiling 1.0R array

    Raw Data Analyzed (1)
    Assay / Reagent collection
    Type
    Title
    ChIP-chip_Furlong_tin_E4-9
    ChIP-chip
    ChIP-chip of tin from D. melanogaster, embyro (2-4 hr AEL).
    Processed Data Analyzed (0)
    Result
    Type
    Title
    Analysis
    Methods
    Reference Genome
    Reference Annotation
    Data analysis

    Peaks were called with TileMap software (v1) after quantile normalization. For each enriched region, probe intensity peaks were identified as extrema on a smoothed curve of the log2-ratio signal. Finally, 200 bp regions centered on identified extremas were defined. Peak calls were lifted over from Dmel_Release_5 to Dmel_Release_6 using the NCBI Genome Remapping tool.

    Comments
    Associated Data
    Size
    Associated features
    814 TF_binding_site(s)
    Download 
    Files
    Additional Information
    Synonyms and Secondary IDs (4)
    Reported As
    Symbol Synonym
    ChIP-chip_tin_E2-4h_organism
    Tin chip-on-chip
    (Zinzen et al., 2009)
    Tinman Binding Peaks at 2-4h AEL
    (Monfort and Furlong, 2015.1.15)
    Name Synonyms
    ChIP-chip peak calls for tin from D. melanogaster, embyro (2-4 hr AEL).
    (Zinzen et al., 2009)
    Secondary FlyBase IDs
      References (2)