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GEO help: Mouse over screen elements for information. |
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| 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
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| 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.
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| Overall design |
Examination of translation in mouse embryonic stem cells and during differentiation into embryoid bodies
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| Contributor(s) |
Ingolia NT, Lareau LF, Weissman JS |
| Citation(s) |
22056041, 23810193 |
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| Submission date |
Jul 21, 2011 |
| Last update date |
Sep 11, 2019 |
| Contact name |
Nicholas T Ingolia |
| E-mail(s) |
ingolia@berkeley.edu, nick@ingolia.org
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| Phone |
510 664 7071
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| Organization name |
University of California, Berkeley
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| Department |
Molecular and Cell Biology
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| Lab |
Ingolia
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| Street address |
1 Barker Hall # 3202
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platforms (2) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (18)
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| 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 |
| GSM765288 |
ES cell 36 hours in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) mrna_mesc_nolif Illumina HiSeq |
| GSM765289 |
ES cell feeder-free, w/ LIF 60 s CYH (100 ug/ml) mrna_mesc_yeslif Illumina GAII |
| GSM765290 |
embryoid body 8d in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) ribo_eb Illumina GAII |
| GSM765291 |
embryoid body 8d in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) ribo_eb Illumina HiSeq |
| GSM765292 |
ES cell feeder-free, w/ LIF 60 s CYH (100 ug/ml) ribo_mesc_chx Illumina GAII |
| GSM765293 |
ES cell feeder-free, w/ LIF 60 s emetine ribo_mesc_emet Illumina GAII |
| GSM765294 |
ES cell feeder-free, w/ LIF 120 s HRT (1 ug/ml) then 60 s CYH (100 ug/ml) ribo_mesc_harr120s Illumina GAII |
| GSM765295 |
ES cell feeder-free, w/ LIF 150 s HRT (1 ug/ml) then 60 s CYH (100 ug/ml) ribo_mesc_harr150s Illumina GAII |
| GSM765296 |
ES cell feeder-free, w/ LIF 180 s HRT (0.5 ug/ml) then 60 s CYH (100 ug/ml) ribo_mesc_harr180s Illumina GAII |
| GSM765297 |
ES cell feeder-free, w/ LIF 90 s HRT (1 ug/ml) then 60 s CYH (100 ug/ul) ribo_mesc_harr90s Illumina GAII |
| GSM765298 |
ES cell feeder-free, w/ LIF none ribo_mesc_nochx Illumina GAII |
| GSM765299 |
ES cell 36 hours in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) ribo_mesc_nolif Illumina GAII |
| GSM765300 |
ES cell 36 hours in low-adhesion dishes w/o LIF 60 s CYH (100 ug/ml) ribo_mesc_nolif Illumina HiSeq |
| GSM765301 |
ES cell feeder-free, w/ LIF 60 s CYH (100 ug/ml) ribo_mesc_yeslif Illumina GAII |
| GSM765302 |
ES cell feeder-free, w/ LIF 60 s CYH (100 ug/ml) ribo_mesc_yeslif Illumina HiSeq |
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| Relations |
| SRA |
SRP007567 |
| BioProject |
PRJNA144149 |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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