Identification of Transcription Factor binding sites by high-throughput ChIP-chip experiments in Drosophila
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Kevin White (PI) Hugo Bellen Robert Grossman Roger Hoskins Manolis Kellis Folker Meyer James Posakony Bing Ren Steven Russell Robert White |
University of Chicago Baylor College of Medicine University of Illinois, Chicago Lawrence Berkeley National Laboratory Massachusetts Institute of Technology Argonne National Lab University of California, San Diego Ludwig Institute University of Cambridge University of Cambridge |
The White Lab is aiming to map the association of all the Drosophila Transcription Factors (TF) and DNA associated proteins on the fly's whole genome. The main technique that will be used for this purpose is ChIP-chip. To achieve this goal, we designed a multi-step pipeline starting from the comprehensive listing of the fly TF to the classification of cis-regulatory modules (CRM). The steps of this pipeline are described in the figure below. The Module 1 aims to produce ChIP-grade antibodies for every TF in the fly genome. After thorough validation these antibodies will be used for the ChIP experiments performed in the Module 2. The ChIP samples produced will then be used to hybridize whole-genome tiling microarays. 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. The Module 3 aims to identify these binding sites, to classify them and to extract biological information by extensive comparaison between the different datasets. Also developed in the computational part of the pipeline is a tracking database called DSTN to help in coordination of the different persons involved in the pipeline.
The details and persons involved in every step of this pipeline are summarized below.
Contact Information
- PI:
- Kevin P. WHITE : kpwhite@uchicago.edu
- Wet lab:
- Nicolas NEGRE : nnegre@bsd.uchicago.edu
- Tong-Ruei LI : tongrueili@uchicago.edu
- Carolyn MORRISON: cmorriso@genetics.bsd.uchicago.edu
- Lionel SENDEROWICZ : email address
- Elizabeth HEINZ : email address
- Informatics:
- Parantu SHAH : pshah2@bsd.uchicago.edu