In Vivo DNA Binding

Browse ChIP/chip Data
Browse ChIP/seq Data
Data Releases

Overview:
   Summary
   Protocols

Software:
   TiMAT
   Secondary
      Analysis Scripts

   Berkeley
      Quantitative
      Genome Browser

Data Releases

We periodically issue new releases of our in vivo DNA binding data. In addition to data on new factors, each release includes information on all factors included in previous releases, but the data may have been reprocessed for these factors through improved analysis pipelines. Each release is a data freeze. No data, meta data or analyses within a freeze will be altered.

Current Release: Our web site allows retrieval only from our most recent data release, currently release 2.1. This release contains ChIP/chip data for 21 of the 37 principal regulators of the early embryo network as well as for Zeste, TFIIB and RNA polymerase as used in MacArthur et al, 2009 and Li et al, 2010. All were processed using TiMAT version 3.4.4 and are mapped to Drosophila Genome Sequence Release 4.0. In addition, the release contains ChIP/seq data 6 of the principal regulators in both D. melanogaster and D. Yakuba, see Bradley et al, 2010 for details.

Previous Releases: Files from old data releases are provided as downloadable tar/gzip files containing summary tables of bound regions and neighboring genes. Our previous data releases are:

Release 1.0. This contains the information on the 6 sequence specific transcription factors and RNA polymerase used in Li et al, 2008. Because these data were run on several different, older versions of TiMAT, we recommend that data on these factors be taken from the current release, 1.1.

Release 1.1. This contains the information on the 6 sequence specific transcription factors and RNA polymerase used in Li et al, 2008 and zeste. All were processed using TiMAT version 3.4.4 and are mapped to Drosophila Genome Sequence Release 4.0.

Release 2.0:This contains ChIP/chip data for 21 of the 37 principal regulators of the early embryo network as well as for Zeste, TFIIB, and RNA polymerase used in MacArthur et al, 2009. All were processed using TiMAT version 3.4.4 and are mapped to Drosophila Genome Sequence Release 4.0.