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Series GSE25107 Query DataSets for GSE25107
Status Public on Jan 19, 2011
Title Native elongating transcript sequencing (NET-seq) of wild type Saccharomyces cerevisiae and of DST1, RCO1, SET1, SET2, EAF3 deletion strains
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Summary We present an approach (native elongating transcript sequencing, NET-seq), based on deep sequencing of 3’ ends of nascent transcripts associated with RNA polymerase, to monitor transcription at nucleotide resolution. Application of NET-seq in Saccharomyces cerevisiae reveals that while promoters are generally capable of divergent transcription, the Rpd3S deacetylation complex enforces strong directionality to most promoters by suppressing antisense transcript initiation. Our studies also reveal pervasive polymerase pausing and backtracking throughout the body of transcripts. Average pause density shows prominent peaks at each of the first four nucleosomes, with the peak location occurring in good agreement with in vitro biophysical measurements. Thus nucleosome-induced pausing represents a major barrier to transcriptional elongation in vivo.
Overall design Examination of nascent transcripts in yeast and mutant strains
Contributor(s) Churchman LS, Weissman JS
Citation(s) 21248844
Submission date Nov 03, 2010
Last update date May 15, 2019
Contact name L. Stirling Stirling Churchman
Organization name University of California-San Francisco
Street address 1700 Fourth St. Byers Hall - Room 404
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platforms (1)
GPL9377 Illumina Genome Analyzer II (Saccharomyces cerevisiae)
Samples (7)
GSM617027 WT_NET-seq
GSM617028 WT_mRNA-seq
GSM617029 RCO1D_NET-seq
SRA SRP004431
BioProject PRJNA134499

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE25107_RAW.tar 69.4 Mb (http)(custom) TAR (of WIG)
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Processed data provided as supplementary file
Raw data are available in SRA

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