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Series GSE13750 Query DataSets for GSE13750
Status Public on Feb 12, 2009
Title Genome-Wide Analysis In Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Organism Saccharomyces cerevisiae
Experiment type Other
Expression profiling by high throughput sequencing
Summary Techniques for systematically monitoring protein translation have lagged far behind methods for measuring mRNA levels. Here we present a ribosome profiling strategy, based on deep sequencing of ribosome protected mRNA fragments, that enables genome-wide investigation of translation with sub-codon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. These studies defined the protein sequences being translated and found extensive translational control both for determining absolute protein abundance and for responding to environmental stress. We also observed distinct phases during translation involving a large decrease in ribosome density going from early to late peptide elongation as well as wide-spread, regulated initiation at non-AUG codons. Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible.
Overall design Examine replicates of ribosome footprints and mRNA abundance in biological replicates of log-phase growth and acute amino acid starvation
Contributor(s) Ingolia NT, Weissman JS, Newman JR, Ghaemmaghami S
Citation(s) 19213877
Submission date Nov 26, 2008
Last update date May 15, 2019
Contact name Nicholas T Ingolia
Phone 410 246 3025
Organization name Carnegie Institution
Department Embryology
Lab Ingolia
Street address 3520 San Martin Drive
City Baltimore
State/province MD
ZIP/Postal code 21218
Country USA
Platforms (1)
GPL9134 Illumina Genome Analyzer (Saccharomyces cerevisiae)
Samples (8)
GSM346111 Footprints-rich-1
GSM346114 Footprints-rich-2
GSM346115 Footprints-starved-1
SRA SRP000637
BioProject PRJNA109405

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Supplementary file Size Download File type/resource
GSE13750_RAW.tar 352.3 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data included within Sample table
Processed data provided as supplementary file

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