ChIP-chip: Histone Modifications in embryo 0-12hr

Embryo 0-12h H3K9me3 ChIP-chip (White project, White subgroup)

Details

Genetic material were isolated from staged Drosophila (y; bw cn sp) embryos at mixed stages between 0-12h, and cross-linked with formaldehyde. After lysis and sonication the chromatin was immunoprecipitated with antibodies recognizing histone H3 trimethylated on lysine 9. The DNA was amplified, labeled, and hybridized to Affy microarrays (mock IP DNA was labelled in parallel and hybridized simultaneously to the same chip). Density plots are the combination of three data sets using MAT. The Joint Binding Deconvolution algorithm was used to predict binding peaks in normalized data from three experimental replicates.

Series 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.
ChIP-seq, meaning direct sequencing of the ChIP sample on the Solexa platform, has also been used to validate some datasets and will become- as the project advances- the main production platform.

To support ChIP-chip and ChIP-seq datasets, and in order to link association of factors to the DNA with regulation of transcription, several RNA-seq (direct sequencing of the transcriptome on the Solexa platform) datasets will be genrated for the time-points under scrutiny.

Protocols

  1. Growth and isolation: Embryonic collection Stage 0-12 hours AEL:KW:1, Embryonic collection Stage 0-12 hours AEL:KW:1,Cross-linking
  2. Sample preparation: White_Lab/IP, Array Scanning, Affymetrix Labeling and Hybridization:KW:1, White_Lab/IP, Whole_Genome_Amplification
  3. Data Processing: MAT analysis

Experimental Reagents

  1. Antibodies: H3K9me3, H3K36me3, No Antibody Control, H3K27me3
  2. Arrays: Affymetrix Drosophila Tiling Arrays v2.0R

Sample Details

  1. Animals/Lines: Embryo 0-12h, Embryo 0-12h


  1. Other Protocols: Cross-linking


  1. Data Analysis: Data Processing:KW:1


Release Date: 2010-01-12 Track 621