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| Status |
Public on Jan 29, 2013 |
| Title |
Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Steady-state gene expression is a coordination of synthesis and decay of RNA through epigenetic regulation, transcription factors, miRNAs, and RNA-binding proteins. Here, we present Bru-Seq and BruChase-Seq to assess genome-wide changes to RNA synthesis and stability in human fibroblasts at homeostasis and after exposure to the proinflammatory TNF. The inflammatory response in human cells involves rapid and dramatic changes in gene expression, and the Bru-Seq and BruChase-Seq techniques revealed a coordinated and complex regulation of gene expression both at the transcriptional and posttranscriptional levels. The combinatory analysis of both RNA synthesis and stability using Bru-Seq and BruChase-Seq allows for a much deeper understanding of mechanisms of gene regulation than afforded by the analysis of steadystate total RNA and should be useful in many biological settings.
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| Overall design |
Analysis of the effect of TNF exposure in nascent gene expression and in transcript stability
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| Contributor(s) |
Paulsen MT, Veloso A, Prasad J, Bedi K, Ljungman EA, Tsan Y, Chang C, Tarrier B, Washburn JG, Lyons R, Robinson DR, Kumar-Sinha C, Wilson TE, Ljungman M |
| Citation(s) |
23345452 |
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| Submission date |
Jan 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Mats Ljungman |
| E-mail(s) |
tenbroek@med.umich.edu, bedik@umich.edu, ivenkat@umich.edu
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| Organization name |
University of Michigan
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| Street address |
NCRC, B520 Room 1346 2800 Plymouth Rd.
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| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109-2800 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA186428 |
| SRA |
SRP017919 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE43440_RAW.tar |
9.9 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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