A high-resolution map of transcription in the yeast genome

This dataset from 2006 has in the meanwhile been superseded by better, bigger and cleaner data. We provide this website for the scientific record. Please see here for the most recent and best-annotated transcriptome data browser, based on the paper by Xu Z., Wei W. et al.

The actinomycin D protocol for avoiding antisense artifacts was described by Fabiana Perocchi et al., Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D, Nucleic Acids Research 2007 35(19):e128.

The segmentation algorithm was described by Huber, Toedling and Steinmetz, Transcript mapping with high-density oligonucleotide tiling arrays, Bioinformatics 2006, 22(16): 1963-1970, and software is available in the tilingArray package in the Bioconductor project.

Segment Tables: Poly(A) RNA and Total RNA. Be patient, the tables are large and take some time to load. For explanation, please see the description and the paper A high-resolution map of transcription in the yeast genome, L. David, W. Huber, M. Granovskaia, J. Toedling, C.J. Palm, L. Bofkin, T. Jones, R. W. Davis, L. M. Steinmetz, PNAS 28 March 2006 describes the data, methods and our results.

The data are provided at ArrayExpress with accession number E-TABM-14. The data are also provided in the R-package davidTiling from the Bioconductor project, which contains cel files and probe to genome mapping. The array reporter sequences are provided in the Bioconductor package Scerevisiaetilingprobe, or equivalently in the Affymetrix probe sequence file S.cerevisiae_tiling.1lq.

There are also a compressed tab-delimited text files of normalized probe intensities: [Poly-A RNA] and [Total RNA]. For genomic positions with a unique probe match, these files contain the probe's normalized mean intensity over the three Poly-A-RNA samples and over the two Total-RNA samples, respectively. Probe spacing is chosen such that adjacent probes are at least 7 bp and no more than 8 bp apart, where posssible.

Contact: Wolfgang Huber