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| Status |
Public on Aug 15, 2015 |
| Title |
Expression dynamics in mammalian cells responding to protein misfolding stress |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
We have employed whole genome microarray expression profiling to track the transcriptome expression change under DTT induced protein misfolding stress.
The relative importance of gene expression regulation at the mRNA versus the protein-level is a matter of ongoing debate. We present an in-depth analysis of a cervical cancer cell line responding to protein misfolding stress induced by dithiothreitol treatment, quantifying the dynamics of mRNA and protein concentrations for >3,500 genes over a time-course 30 hours. While the early phase of the experiment (<two hours) was marked by apoptosis, surviving cells were marked by a strong response to unfolded proteins and stress of the endoplasmatic reticulum, specifically during the intermediate phase (two to eight hours). Using statistical time series analysis, we detected significant changes in the regulatory parameters at the RNA-level, caused by transcription and mRNA degradation, and at the protein-level, caused by translation and protein degradation. mRNA- and protein-level regulation were of equal importance (XX and YYY%, respectively), but displayed different magnitudes and dynamics: mRNA fold changes were much smaller on average than those of the proteins. While our method did not capture immediate changes, we found the strongest regulatory response between two and eight hours after the treatment. mRNA-level regulation showed a spike around this time interval, while protein-level regulation was delayed and continued at slower pace until the end of the experiment.
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| Overall design |
RNA expression in HeLa cell line was measured at 0, 0.5, 1, 2, 8, 16, 24, 30 hrs after exposure to 2.5mM DTT. Two biological replicates were conducted.
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| Contributor(s) |
Cheng Z, Krueger S, Rock T, Vogel C |
| Citation(s) |
26792871 |
| Submission date |
Apr 15, 2015 |
| Last update date |
Nov 27, 2018 |
| Contact name |
Zhe Cheng |
| E-mail(s) |
zhecheng2010@gmail.com
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| Phone |
2129983658
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| Organization name |
New York University
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| Department |
Bilogy Department
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| Lab |
Christine Vogel lab
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| Street address |
12 Waverly Place, 4th Floor
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10003 |
| Country |
USA |
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| Platforms (1) |
| GPL13607 |
Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Feature Number version) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA281173 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE67901_RAW.tar |
54.6 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE67901_normalized_ENSG_IDs.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE67901_normalized_ENSG_IDs_log_filtered_LOWESSsmoothed.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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