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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 06, 2015 |
| Title |
Dynamic profiling of the protein life cycle in response to pathogens (protein) |
| Organism |
Mus musculus |
| Experiment type |
Protein profiling by Mass Spec
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| Summary |
Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle.
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| Overall design |
Mouse primary dendritic cells were treated with LPS or mock stimulus and profiled over a 12-hour time course. Cells were grown in M-labeled SILAC media, which was replaced with H-labeled SILAC media at time 0. Aliquots were taken at 0, 0.5, 1, 2, 3, 4, 5, 6, 9, and 12 hours post-stimulation and added to equal volumes of a master mix of unlabeled (L) cells for the purpose of normalization. RNA-Seq was performed at 0, 1, 2, 4, 6, 9, and 12 hours post-stimulation.
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| Contributor(s) |
Jovanovic M, Rooney MS, Hacohen N, Regev A |
| Citation(s) |
25745177 |
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| Submission date |
Jul 25, 2014 |
| Last update date |
Mar 12, 2015 |
| Contact name |
Catherine J Wu |
| Organization name |
Dana Farber Cancer Institute
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| Lab |
Wu Lab
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| Street address |
450 Brookline Ave.
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platforms (1) |
| GPL18998 |
LC-MS/MS on Orbitrap Q Exactive |
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| Samples (88)
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| GSM1446461 |
Replicate 1, Medium channel SILAC, time 0 |
| GSM1446462 |
Replicate 1, Medium channel SILAC, Mock-stimulus, time 0.5h |
| GSM1446463 |
Replicate 1, Medium channel SILAC, Mock-stimulus, time 1h |
| GSM1446464 |
Replicate 1, Medium channel SILAC, Mock-stimulus, time 2h |
| GSM1446465 |
Replicate 1, Medium channel SILAC, Mock-stimulus, time 3h |
| GSM1446466 |
Replicate 1, Medium channel SILAC, Mock-stimulus, time 4h |
| GSM1446467 |
Replicate 1, Medium channel SILAC, Mock-stimulus, time 5h |
| GSM1446468 |
Replicate 1, Medium channel SILAC, Mock-stimulus, time 6h |
| GSM1446469 |
Replicate 1, Medium channel SILAC, Mock-stimulus, time 9h |
| GSM1446470 |
Replicate 1, Medium channel SILAC, Mock-stimulus, time 12h |
| GSM1446471 |
Replicate 1, Medium channel SILAC, Mock-stimulus, time 24h |
| GSM1446472 |
Replicate 1, Medium channel SILAC, LPS-stimulus, time 0.5h |
| GSM1446473 |
Replicate 1, Medium channel SILAC, LPS-stimulus, time 1h |
| GSM1446474 |
Replicate 1, Medium channel SILAC, LPS-stimulus, time 2h |
| GSM1446475 |
Replicate 1, Medium channel SILAC, LPS-stimulus, time 3h |
| GSM1446476 |
Replicate 1, Medium channel SILAC, LPS-stimulus, time 4h |
| GSM1446477 |
Replicate 1, Medium channel SILAC, LPS-stimulus, time 5h |
| GSM1446478 |
Replicate 1, Medium channel SILAC, LPS-stimulus, time 6h |
| GSM1446479 |
Replicate 1, Medium channel SILAC, LPS-stimulus, time 9h |
| GSM1446480 |
Replicate 1, Medium channel SILAC, LPS-stimulus, time 12h |
| GSM1446481 |
Replicate 1, Medium channel SILAC, LPS-stimulus, time 24h |
| GSM1446482 |
Replicate 2, Medium channel SILAC, time 0 |
| GSM1446483 |
Replicate 2, Medium channel SILAC, Mock-stimulus, time 0.5h |
| GSM1446484 |
Replicate 2, Medium channel SILAC, Mock-stimulus, time 1h |
| GSM1446485 |
Replicate 2, Medium channel SILAC, Mock-stimulus, time 2h |
| GSM1446486 |
Replicate 2, Medium channel SILAC, Mock-stimulus, time 3h |
| GSM1446487 |
Replicate 2, Medium channel SILAC, Mock-stimulus, time 4h |
| GSM1446488 |
Replicate 2, Medium channel SILAC, Mock-stimulus, time 5h |
| GSM1446489 |
Replicate 2, Medium channel SILAC, Mock-stimulus, time 6h |
| GSM1446490 |
Replicate 2, Medium channel SILAC, Mock-stimulus, time 9h |
| GSM1446491 |
Replicate 2, Medium channel SILAC, Mock-stimulus, time 12h |
| GSM1446492 |
Replicate 2, Medium channel SILAC, Mock-stimulus, time 24h |
| GSM1446493 |
Replicate 2, Medium channel SILAC, LPS-stimulus, time 0.5h |
| GSM1446494 |
Replicate 2, Medium channel SILAC, LPS-stimulus, time 1h |
| GSM1446495 |
Replicate 2, Medium channel SILAC, LPS-stimulus, time 2h |
| GSM1446496 |
Replicate 2, Medium channel SILAC, LPS-stimulus, time 3h |
| GSM1446497 |
Replicate 2, Medium channel SILAC, LPS-stimulus, time 4h |
| GSM1446498 |
Replicate 2, Medium channel SILAC, LPS-stimulus, time 5h |
| GSM1446499 |
Replicate 2, Medium channel SILAC, LPS-stimulus, time 6h |
| GSM1446500 |
Replicate 2, Medium channel SILAC, LPS-stimulus, time 9h |
| GSM1446501 |
Replicate 2, Medium channel SILAC, LPS-stimulus, time 12h |
| GSM1446502 |
Replicate 2, Medium channel SILAC, LPS-stimulus, time 24h |
| GSM1446503 |
Replicate 1, Heavy channel SILAC, time 0 |
| GSM1446504 |
Replicate 1, Heavy channel SILAC, Mock-stimulus, time 0.5h |
| GSM1446505 |
Replicate 1, Heavy channel SILAC, Mock-stimulus, time 1h |
| GSM1446506 |
Replicate 1, Heavy channel SILAC, Mock-stimulus, time 2h |
| GSM1446507 |
Replicate 1, Heavy channel SILAC, Mock-stimulus, time 3h |
| GSM1446508 |
Replicate 1, Heavy channel SILAC, Mock-stimulus, time 4h |
| GSM1446509 |
Replicate 1, Heavy channel SILAC, Mock-stimulus, time 5h |
| GSM1446510 |
Replicate 1, Heavy channel SILAC, Mock-stimulus, time 6h |
| GSM1446511 |
Replicate 1, Heavy channel SILAC, Mock-stimulus, time 9h |
| GSM1446512 |
Replicate 1, Heavy channel SILAC, Mock-stimulus, time 12h |
| GSM1446513 |
Replicate 1, Heavy channel SILAC, Mock-stimulus, time 24h |
| GSM1446514 |
Replicate 1, Heavy channel SILAC, LPS-stimulus, time 0.5h |
| GSM1446515 |
Replicate 1, Heavy channel SILAC, LPS-stimulus, time 1h |
| GSM1446516 |
Replicate 1, Heavy channel SILAC, LPS-stimulus, time 2h |
| GSM1446517 |
Replicate 1, Heavy channel SILAC, LPS-stimulus, time 3h |
| GSM1446518 |
Replicate 1, Heavy channel SILAC, LPS-stimulus, time 4h |
| GSM1446519 |
Replicate 1, Heavy channel SILAC, LPS-stimulus, time 5h |
| GSM1446520 |
Replicate 1, Heavy channel SILAC, LPS-stimulus, time 6h |
| GSM1446521 |
Replicate 1, Heavy channel SILAC, LPS-stimulus, time 9h |
| GSM1446522 |
Replicate 1, Heavy channel SILAC, LPS-stimulus, time 12h |
| GSM1446523 |
Replicate 1, Heavy channel SILAC, LPS-stimulus, time 24h |
| GSM1446524 |
Replicate 2, Heavy channel SILAC, time 0 |
| GSM1446525 |
Replicate 2, Heavy channel SILAC, Mock-stimulus, time 0.5h |
| GSM1446526 |
Replicate 2, Heavy channel SILAC, Mock-stimulus, time 1h |
| GSM1446527 |
Replicate 2, Heavy channel SILAC, Mock-stimulus, time 2h |
| GSM1446528 |
Replicate 2, Heavy channel SILAC, Mock-stimulus, time 3h |
| GSM1446529 |
Replicate 2, Heavy channel SILAC, Mock-stimulus, time 4h |
| GSM1446530 |
Replicate 2, Heavy channel SILAC, Mock-stimulus, time 5h |
| GSM1446531 |
Replicate 2, Heavy channel SILAC, Mock-stimulus, time 6h |
| GSM1446532 |
Replicate 2, Heavy channel SILAC, Mock-stimulus, time 9h |
| GSM1446533 |
Replicate 2, Heavy channel SILAC, Mock-stimulus, time 12h |
| GSM1446534 |
Replicate 2, Heavy channel SILAC, Mock-stimulus, time 24h |
| GSM1446535 |
Replicate 2, Heavy channel SILAC, LPS-stimulus, time 0.5h |
| GSM1446536 |
Replicate 2, Heavy channel SILAC, LPS-stimulus, time 1h |
| GSM1446537 |
Replicate 2, Heavy channel SILAC, LPS-stimulus, time 2h |
| GSM1446538 |
Replicate 2, Heavy channel SILAC, LPS-stimulus, time 3h |
| GSM1446539 |
Replicate 2, Heavy channel SILAC, LPS-stimulus, time 4h |
| GSM1446540 |
Replicate 2, Heavy channel SILAC, LPS-stimulus, time 5h |
| GSM1446541 |
Replicate 2, Heavy channel SILAC, LPS-stimulus, time 6h |
| GSM1446542 |
Replicate 2, Heavy channel SILAC, LPS-stimulus, time 9h |
| GSM1446543 |
Replicate 2, Heavy channel SILAC, LPS-stimulus, time 12h |
| GSM1446544 |
Replicate 2, Heavy channel SILAC, LPS-stimulus, time 24h |
| GSM1446545 |
Replicate 1, Unlabeled, Baseline, AspN Peptide Library Protocol |
| GSM1446546 |
Replicate 2, Unlabeled, Baseline, AspN Peptide Library Protocol |
| GSM1446547 |
Replicate 1, Unlabeled, Baseline, LysN Peptide Library Protocol |
| GSM1446548 |
Replicate 2, Unlabeled, Baseline, LysN Peptide Library Protocol |
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| This SubSeries is part of SuperSeries: |
| GSE59793 |
Dynamic profiling of the protein life cycle in response to pathogens |
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| Relations |
| BioProject |
PRJNA256212 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE59792_proteinGroups_IBAQ_DC0h_AspN.txt.gz |
993.6 Kb |
(ftp)(http) |
TXT |
| GSE59792_proteinGroups_IBAQ_DC0h_LysN.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE59792_proteinGroups_IBAQ_fullexperiment_Trypsin.txt.gz |
35.6 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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