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Series GSE59784 Query DataSets for GSE59784
Status Public on Mar 06, 2015
Title Dynamic profiling of the protein life cycle in response to pathogens (RNA-seq)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
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.
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.
Contributor(s) Jovanovic M, Rooney MS, Hacohen N, Regev A
Citation(s) 25745177
Submission date Jul 25, 2014
Last update date May 15, 2019
Contact name Catherine J Wu
Organization name Dana Farber Cancer Institute
Lab Wu Lab
Street address 450 Brookline Ave.
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (28)
GSM1446348 Replicate 1, RNA-Seq, time 0
GSM1446349 Replicate 1, RNA-Seq, Mock-stimulus, time 1h
GSM1446350 Replicate 1, RNA-Seq, Mock-stimulus, time 2h
This SubSeries is part of SuperSeries:
GSE59793 Dynamic profiling of the protein life cycle in response to pathogens
BioProject PRJNA256196
SRA SRP044873

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Supplementary file Size Download File type/resource
GSE59784_ribosomalprofiling.txt.gz 99.8 Kb (ftp)(http) TXT
GSE59784_rna.norm.txt.gz 495.4 Kb (ftp)(http) TXT
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