ChIP-chip: Histone Modifications in embryo 16-20hr

Embryo 16-20h H3K9Me3 ChIP-chip (White project)


Nuclei were isolated from staged Drosophila (y; bw cn sp) embryos, 16 - 20 hr after egg laying, and cross-linked with formaldehyde. After lysis and sonication the chromatin was immunoprecipitated with affinity-purified antibodies recognizing histone H3 trimethylated on lysine 9. The DNA was amplified, labeled, and hybridized to Agilent microarrays (mock IP DNA was labelled in parallel and hybridized simultaneously to the same chip). The Joint Binding Deconvolution algorithm was used to predict binding peaks in normalized data from three experimental replicates.

General Description

The White Lab is aiming to map the association of all the Transcription Factors (TF) and DNA associated proteins on the genome of Drosophila melanogaster. The main technique that will be used for this purpose is chromatin immunoprecipitation-on-chip (ChIP-on-chip) utilizing whole-genome tiling arrays. The data generated by ChIP-chip experiments consist basically of a plot of signal intensity across the genome. The highest signals correspond to positions in the genome occupied by the tested TF.


  1. Growth and isolation: E16-20 collection histone timecourse:KW:1
  2. Sample preparation: White_Lab/IP, Whole_Genome_Amplification, Agilent 244K ChIP Labeling:KW:1, Array Hybridization for ChIP-chip:KW:1, Array Scanning
  3. Data Analysis: Agilent ChIP data processing:KW:1, Agilent ChIP peak finding:KW:1
  4. Other Protocols: Cross-linking

Experimental Reagents

  1. Antibodies: H3K9me3, No Antibody Control
  2. Arrays: Agilent Drosophila tiling array 1 of 3, Agilent Drosophila tiling array 2 of 3, Agilent Drosophila tiling array 3 of 3

Sample Details

  1. Animals/Lines: Embryo 16-20h, Drosophila melanogaster, E16-20_H3K9Me3_1_1, E16-20_H3K9Me3_1_2, E16-20_H3K9Me3_1_3, E16-20_H3K9Me3_2_1, E16-20_H3K9Me3_2_2, E16-20_H3K9Me3_2_3, E16-20_H3K9Me3_3_1, E16-20_H3K9Me3_3_2, E16-20_H3K9Me3_3_3

Release Date: 2010-01-12