Hesselberth 2009, Global mapping of protein-DNA interactions


Protein occupancy on genomic DNA in yeast by dense mapping of individual DNase I cleavages from intact nuclei.


Data have been downloaded from Noble Research Lab
Input file format: BED


From Yeast Apr 2011 (NCBI3.1/sacCer3) Assembly

Filename Description Feature GEO-ID
1 yeast_DNaseI_sacCer3.sga Yeast DNaseI DNaseI -

Technical Notes

BED files were dowloaded from Noble Research Lab and processed with in-house software to make SGA files:

  1. Import source file:
    wget http://noble.gs.washington.edu/proj/footprinting/yeast.dnaseI.tagCounts.bed
  2. Generate SGA files:
    wget http://hgdownload.cse.ucsc.edu/goldenPath/sacCer1/liftOver/sacCer1ToSacCer3.over.chain.gz
    gunzip sacCer1ToSacCer3.over.chain.gz
    liftOver yeast.dnaseI.tagCounts.bed sacCer1ToSacCer3.over.chain yeast_DNaseI_sacCer3.bed unMapped.tags
  3. awk 'BEGIN{
       while ((getline < "/db/genome/sacCer3/chr_NC_gi") > 0)
          chr[$1] = $2
       sub("chr", "", $1);
       if ($1 in chr){
          print chr[$1], "DNaseI", $2, "-", $5;
          print chr[$1], "DNaseI", $3, "+", $5;
    }' yeast_DNaseI_sacCer3.bed | sort -s -k1,1 -k3,3n -k4,4 -T . | compactsga > yeast_DNaseI_sacCer3.sga


  1. Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA.
    Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods. 2009 Apr;6(4):283-9. Epub 2009 Mar 22. PMID: 19305407