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This document briefly describes the data file types available from the Auble Lab web site pertaining to
 

Summary: Auble Lab
This document briefly describes the data file types available from the Auble Lab
web site pertaining to:
K. Poorey, R.O. Sprouse, M.N. Wells, R. Viswanathan, S. Bekiranov, and D.T.
Auble. RNA Synthesis Precision Is Regulated by Preinitiation Complex Turnover.
Genome Res. 20:1679-1688, 2010.
If you have a question about these files or formats please send your query to
David Auble: auble@virginia.edu
All of these files are compatible with IGB (Integrated genome Browser) available
at the Affymetrix website.
File types:
.sgr: graph files representing absolute RNA signal or ChIP occupancy
levels computed by the TAS program.
They are in the format: Chromosome Genomic Coordinate Signal Value
For the absolute total RNA for WT (MOT1), WT (SET2), mot1-42, and set2
strains, the data was smoothed over a 100 bp window. For the differential RNA
(log2(mutant/WT)) the data was smoothed over a 500 bp window.
For the TBP and TFIIB whole genome ChIP-Chip studies, the data was
smoothed over a 500 bp window.
This format is also used to display the TBP and TFIIB ChIP-chip peak locations.

  

Source: Auble, David - Department of Biochemistry and Molecular Genetics, University of Virginia

 

Collections: Biology and Medicine