Hesselberth 2009, Global mapping of protein-DNA interactions

Description

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

Source

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

Samples

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{
       FS="\t";
       OFS="\t";
       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
    

References

  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