Rhee_2012_PMID_22258509.README Last modified: 2016-06-17 Rhee HS, Pugh BF (2012) Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature 483(7389):295-301 PMID: 22258509 Rhee et al. applied a high-resolution sequencing ChIP-based method called ChIP-exo to profile the structural and positional organization of transcription pre-initiation complexes (RNA polymerase II, protein complexes TFIIA, TFIIB, TFIID (or TBP), TFIIE, TFIIF, TFIIH and TFIIK) across the budding yeast genome. Their technique enabled identification of TATA-like elements at "TATA-less" promoters. A short summary of the contents of each data file compiled by SGD can be found in the following secion. More in depth details can be found within the file header of each file. Data files last modified: April 9, 2012 SGD has compiled the following data files from this publication: * Rhee_2012_TATA_elements_V64.gff3 * Rhee_2012_TATA_less_features_V55.tab These files were compiled from Supplementary data file S1 accompanying the publication, containing a list of the top 6,045 PICs, separated here into 5,947 TATA-element containing and 98 TATA-less features according to the classification published by the authors by SGD. The sequencing reads were mapped to SGD V55 (January 19, 2007) version of the S. cerevisiae genome by the authors and lifted over to the latest version (SGD V64, February 2011) by SGD. Note that the coordinate position values in the Rhee_2012_TATA_less_features_V55.tab are the original published coordinates against genome version V55 and are not lifted over to the newest genome version. Features that were not mappable to V64 are listed in the file: * Rhee_2012_TATA_elements_V55toV64_unmapped.txt The original V55 sequencing reads are in: * Rhee_2012_TATA_elements_V55.gff3 Additional supplementary information: NCBI Sequence read archive accession: SRA046523 http://www.ncbi.nlm.nih.gov/sra?term=SRA046523