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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 16, 2007 |
| Title |
Expression data from spec. transcriptional activity of primary mouse embryonic fibroblasts (MEF) in response to serum. |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
Current methods to analyze gene expression measure steady-state levels of mRNA. In order to specifically analyze mRNA transcription, a technique has been developed that can be applied in-vivo. The technique is referred with the acronym NIAC-NTR (Non Invasive Application and Capture of Newly Transcribed RNA). This method makes use of the cellular pyrimidine salvage pathway and is based on affinity-chromatographic isolation of thiolated mRNA. When combined with data on mRNA steady-state levels, this method is able to assess the relative contributions of mRNA synthesis and degradation/stabilization. It overcomes limitations associated with currently available methods such as mechanistic intervention that disrupts cellular physiology, or the inability to apply the techniques in-vivo. The method has been applied to a model of serum response of cultured primary mouse embryonic fibroblasts.
Affymetrix GeneChip microarrays were used to detail regulatory mechanisms of mRNA expression and the relative contributions of RNA synthesis and turnover within distinct pathways, and identification of genes expressed at low abundance at the transcriptional level.
Keywords: treatment experiment
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| Overall design |
The gene expression and regulation program at the RNA level early (2h) in response to serum was studied. Total RNA, amplified total RNA and specifically enriched newly transcribed RNA was isolated from serum starved and 2h serum treated MEF cells. This experiment allowed detailed regulatory mechanisms of mRNA expression and the relative contributions of RNA synthesis and turnover within distinct pathways, and identification of genes expressed at low abundance at the transcriptional level of MEF cells early in response to serum.
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| Contributor(s) |
Kenzelmann M, Maertens S, Hergenhahn M, Küffer S, Hotz-Wagenblatt A, Li L, Wang S, Ittrich C, Lemberger T, Arribas R, Jonnakuty S, Hollstein M, Schmid W, Gretz N, Gröne H, Schütz G |
| Citation(s) |
17405863 |
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| Submission date |
Jan 10, 2007 |
| Last update date |
Feb 18, 2018 |
| Contact name |
Marc Kenzelmann |
| E-mail(s) |
[email protected]
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| Phone |
+41 31 632 3251
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| Fax |
+41 31 632 3550
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| Organization name |
Institute of Medical Microbiology, University of Bern
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| Department |
Molecular Genome Analysis
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| Street address |
Friedbuhlstrasse 51
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| City |
Bern |
| ZIP/Postal code |
3010 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL81 |
[MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array |
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| Samples (23)
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| GSM154514 |
Serum starved MEF, amplified total RNA, biological rep1 |
| GSM154515 |
Serum treated MEF, amplified total RNA, biological rep1 |
| GSM154516 |
Serum starved MEF, amplified total RNA, biological rep2 |
| GSM154517 |
Serum treated MEF, amplified total RNA, biological rep2 |
| GSM154518 |
Serum treated MEF, amplified total RNA, biological rep3 |
| GSM154519 |
Serum starved MEF, amplified total RNA, biological rep3 |
| GSM154520 |
Serum treated MEF, amplified total RNA, biological rep4 |
| GSM154521 |
Serum starved MEF, newly transcribed RNA, biological rep1 |
| GSM154522 |
Serum treated MEF, newly transcribed RNA, biological rep1 |
| GSM154523 |
Serum starved MEF, newly transcribed RNA, biological rep2 |
| GSM154524 |
Serum treated MEF, newly transcribed RNA, biological rep2 |
| GSM154525 |
Serum starved MEF, newly transcribed RNA, biological rep3 |
| GSM154526 |
Serum treated MEF, newly transcribed RNA, biological rep3 |
| GSM154527 |
Serum starved MEF, newly transcribed RNA, biological rep4 |
| GSM154528 |
Serum treated MEF, newly transcribed RNA, biological rep4 |
| GSM154529 |
Serum starved MEF, total RNA, biological rep1 |
| GSM154530 |
Serum treated MEF, total RNA, biological rep1 |
| GSM154531 |
Serum starved MEF, total RNA, biological rep2 |
| GSM154532 |
Serum treated MEF, total RNA, biological rep2 |
| GSM154533 |
Serum starved MEF, total RNA, biological rep3 |
| GSM154534 |
Serum treated MEF, total RNA, biological rep3 |
| GSM154535 |
Serum starved MEF, total RNA, biological rep4 |
| GSM154536 |
Serum treated MEF, total RNA, biological rep4 |
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| Relations |
| BioProject |
PRJNA99005 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE6697_RAW.tar |
63.6 Mb |
(http)(custom) |
TAR (of CEL) |
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