Supplemental information for Genomewide identification of spliced introns using a tiling microarray

Z. Zhang, J. Hesselberth and S. Fields

This page contains supplemental information useful for the visulatization of intronic regions found in yeast using tiling microarrays. All files are in UCSC Genome Browser-compatible formats (BED and WIG) and compressed using Bzip2. All chromosome coordinates are based on the October 2003 Saccharomyces cerevisiae genome draft, which is the version currently used by the UCSC genome browser (http://genome.ucsc.edu).

Descriptions of files available:

• Reference_intron_OCT_2003.bed.bz2 Reference list of introns used in this study.


• Sc-splice-signals.bed.bz2 Whole genome survey of 5' splicing signals and branchpoint signals in S. cerevisiae compiled from SGD and Spingola et al, (1999) RNA.


• ZZ137-ZZ248-bw20_pvalue.00058_fdr.10.bed.bz2 Significant probe positions at an estimated FDR of 10% (P < 0.00058)


• ZZ137-ZZ248-bw20_pvalue.00028_fdr.05.bed.bz2 Significant probe positions at an estimated FDR of 5% (P < 0.00028)


• ZZ137-ZZ248-bw20_pvalue1E-6_fdr.01.bed.bz2 Significant probe positions at an estimated FDR of 1% (P < 1E-6)


• ZZ137-bw20-sigscale0-signal.wiggle.bz2 Normalised probe intensities of the DBR+ strain (BY4743) from the tiling arrays


• ZZ248-bw20-sigscale0-signal.wiggle.bz2 The normalised probe intensities of the dbr1 strain from the tiling arrays


• ZZ137-ZZ248-bw20-sigscale2-signal-ratio.wiggle.bz2 The log2 ratios of dbr1/DBR+ using normalised probe intensities from the tiling arrays


• RT-PCR-confirmation.psl.bz2 Splice forms confirmed by RT-PCR.


• multiple_hits_probes_translated.bed.bz2 Probes with multiple (n>1), perfect matches to the S. cerevisiae genome. This track is "hidden" by default.


• probe_coverage_translated_by_region.bz2 Tiling array probe coverage of the S. cerevisiae genome. This track is "hidden" by default.

The above files can be uploaded into the UCSC Browser by navigating to the S.cerevisiae genome, clicking "Custom Tracks", and pasting the following lines into the browser. Please note: Some of these files are big, and upload can take 1-2 minutes depending on server traffic.

http://depts.washington.edu/sfields/supplemental_data/intron_tiling_supplement/Reference_intron_OCT_2003.bed.bz2
http://depts.washington.edu/sfields/supplemental_data/intron_tiling_supplement/ZZ137-ZZ248-bw20_pvalue.00058_fdr.10.bed.bz2
http://depts.washington.edu/sfields/supplemental_data/intron_tiling_supplement/ZZ137-ZZ248-bw20_pvalue.00028_fdr.05.bed.bz2
http://depts.washington.edu/sfields/supplemental_data/intron_tiling_supplement/ZZ137-ZZ248-bw20_pvalue1E-6_fdr.01.bed.bz2
http://depts.washington.edu/sfields/supplemental_data/intron_tiling_supplement/Sc-splice-signals.bed.bz2
http://depts.washington.edu/sfields/supplemental_data/intron_tiling_supplement/ZZ137-bw20-sigscale0-signal.wiggle.bz2
http://depts.washington.edu/sfields/supplemental_data/intron_tiling_supplement/ZZ248-bw20-sigscale0-signal.wiggle.bz2
http://depts.washington.edu/sfields/supplemental_data/intron_tiling_supplement/ZZ137-ZZ248-bw20-sigscale2-signal-ratio.wiggle.bz2
http://depts.washington.edu/sfields/supplemental_data/intron_tiling_supplement/RT-PCR-confirmation.psl.bz2
http://depts.washington.edu/sfields/supplemental_data/intron_tiling_supplement/multiple_hits_probes_translated.bed.bz2
http://depts.washington.edu/sfields/supplemental_data/intron_tiling_supplement/probe_coverage_translated_by_region.bz2