GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE34473 Query DataSets for GSE34473
Status Public on Sep 13, 2012
Title Chromatin based modeling of transcription rates identifies the contribution of different regulatory layers to steady-state mRNA levels.
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Messenger RNA levels in eukaryotes are balanced by two consecutive regulatory layers. Primary, transcriptional regulation at the level of chromatin and secondary, post-transcriptional regulation of the initial transcript in the cytoplasm. Each layer is individually studied in mechanistic detail, while integration of both processes is required to quantify the individual contribution to steady-state RNA levels. Here we show that chromatin features are sufficient to model transcription rate but with different sensitivities in dividing versus post mitotic cells. In both cases chromatin derived transcript levels explains over 80% of variance in measured RNA level enabling to separate transcription from different post-transcriptional processes. By further inclusion of measurements of mRNA half-life and micro RNA expression data we identify a low quantitative contribution of RNA decay by either micro RNA or general differential turnover to final mRNA levels. Together this establishes a chromatin based quantitative model for the contribution of transcriptional and posttranscriptional processes to steady-state levels of messenger RNA.
Overall design Strand specific expression profiling by high throughput sequencing.
Contributor(s) Tippmann SC, Ivanek R, Gaidatzis D, Schöler A, van Nimwegen E, Stadler PF, Stadler M, Schübeler D
Citation(s) 22806141
Submission date Dec 15, 2011
Last update date May 15, 2019
Contact name Dirk Schuebeler
Organization name Friedrich Miescher Institute for Biomedical Research
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (6)
GSM778487 ES RNA a
GSM778488 ES RNA b
GSM778489 NP RNA a
BioProject PRJNA174597

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE34473_RAW.tar 71.3 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data provided as supplementary file
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap