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| Status |
Public on Aug 29, 2016 |
| Title |
Fraction-wise RNA-seq of the Salmonella Typhimurium SL1344 cell lysate resolved on a 10-40% glycerol gradient |
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
While many general RNA-binding proteins have been described in eukaryotes, the small RNA chaperone Hfq and the translational regulator CsrA remain the only known global RNA-associated cofactors involved in the bacterial post-transcriptional gene expression control. Here, using an RNA-seq-based analysis of the biochemically partitioned ensemble of cellular RNAs, we uncovered a large group of transcripts that interact with the RNA-binding protein ProQ in Salmonella enterica. We show that ProQ is a conserved abundant protein with a wide range of targets, including a new class of ProQ-associated small RNAs, and predicted functions in many cellular pathways. ProQ preferentially associates with highly structured RNAs, filling the so-far vacant niche of a global double-stranded RNA-binding protein and expanding the range of the post-transcriptional regulation in bacteria." This dataset is a representative experiment carried out to characterize sedimentation properties of bacterial transcripts genome-wide. Downstream analysis of their sedimentation profiles enables their biochemical classification and is a prerequisite for identification of global RNA-binding proteins.
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| Overall design |
The set includes 20 samples corresponding to gradient fractions numbered from the top to the bottom of the gradient. Each fraction is spiked-in with an artificial RNA to enable normalization.
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| Contributor(s) |
Smirnov A, Reinhardt R, Günster R, Förstner KU, Becher D, Vogel J |
| Citation(s) |
27671629 |
| |
| Submission date |
Nov 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Konrad U. Förstner |
| E-mail(s) |
foerstner@zbmed.de
|
| Organization name |
ZB MED - Information Centre for Life Sciences
|
| Department |
Information Services
|
| Lab |
Förstner Lab
|
| Street address |
Gleueler Str. 60
|
| City |
Cologne |
| State/province |
North Rhine-Westphalia |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
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| Platforms (1) |
| GPL17070 |
Illumina HiSeq 2000 (Salmonella enterica subsp. enterica serovar Typhimurium) |
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| Samples (20)
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| This SubSeries is part of SuperSeries: |
| GSE62988 |
Partitioning of a RNA interactome by gradient profiling (Grad-seq) |
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| Relations |
| BioProject |
PRJNA266347 |
| SRA |
SRP049525 |
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