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Series GSE30839 Query DataSets for GSE30839
Status Public on Nov 03, 2011
Title Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Other
Summary The ability to sequence genomes has far outstripped approaches for deciphering the information they encode. Here we present a suite of techniques, based on ribosome profiling (the deep-sequencing of ribosome-protected mRNA fragments), to provide genome-wide maps of protein synthesis as well as a pulse-chase strategy for determining rates of translation elongation. We exploit the propensity of harringtonine to cause ribosomes to accumulate at sites of translation initiation together with a machine learning algorithm to define protein products systematically. Analysis of translation in mouse embryonic stem cells reveals thousands of strong pause sites and novel translation products. These include amino-terminal extensions and truncations and upstream open reading frames with regulatory potential, initiated at both AUG and non-AUG codons, whose translation changes after differentiation. We also define a new class of short, polycistronic ribosome-associated coding RNAs (sprcRNAs) that encode small proteins. Our studies reveal an unanticipated complexity to mammalian proteomes.
 
Overall design Examination of translation in mouse embryonic stem cells and during differentiation into embryoid bodies
 
Contributor(s) Ingolia NT, Lareau LF, Weissman JS
Citation(s) 22056041, 23810193
Submission date Jul 21, 2011
Last update date Sep 11, 2019
Contact name Nicholas T Ingolia
E-mail(s) nick@ingolia.org
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 (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (18)
GSM765285 embryoid body 8d in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) mrna_eb Illumina GAII
GSM765286 embryoid body 8d in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) mrna_eb Illumina HiSeq
GSM765287 ES cell 36 hours in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) mrna_mesc_nolif Illumina GAII
Relations
SRA SRP007567
BioProject PRJNA144149

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE30839_GSM765295_ribo_mesc_harr150s-profiles.tar.gz 15.6 Mb (ftp)(http) TAR
GSE30839_GSM765298_ribo_mesc_nochx-profiles.tar.gz 26.4 Mb (ftp)(http) TAR
GSE30839_RAW.tar 36.4 Gb (http)(custom) TAR (of TXT)
GSE30839_readme.txt 1.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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