|
| Status |
Public on Dec 04, 2014 |
| Title |
Identification of Hfq bound RNA by co-immunoprecipitation and RNA-sequencing |
| Organism |
Agrobacterium tumefaciens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Co-immunoprecipitation with endogenous Hfq3xFlag in exponential, stationary, non-induced and virulence induced conditions, followed by RNA-sequencing, revealed 1697 mRNAs and 208 ncRNAs associated with Hfq. We identified 56 new ncRNAs and validated 3 Hfq-dependent trans sRNAs on by Northern blot analysis. Interestingly, 55% of the ncRNAs were encoded antisense to a protein coding sequence. Abundance of 4 asRNAs and their corresponding target mRNAs was altered upon hfq, indicating a substantial influence of Hfq on asRNA-target interactions.
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| Overall design |
8 cDNA libraries were sequenced. A. tumefaciens hfq3xFlag and hfqWT (control) strains were grown to stationary and exponential growth phase and under non-induced and virulence induced conditions.
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| Contributor(s) |
Möller P, Overlöper A, Förstner K, Wen T, Sharma C, Lai E, Narberhaus F |
| Citation(s) |
25330313 |
| |
| Submission date |
Jul 07, 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 |
| |
|
| Platforms (1) |
| GPL18897 |
Illumina HiSeq 2500 (Agrobacterium tumefaciens) |
|
| Samples (8)
|
| GSM1428954 |
control from OD 0.5 (exponential) conditions |
| GSM1428955 |
Hfq-bound RNA from OD 0.5 (exponential) conditions |
| GSM1428956 |
control from OD 1.0 (exponential) conditions |
| GSM1428957 |
Hfq-bound RNA from OD 1.0 (exponential) conditions |
| GSM1428958 |
control from -Vir (non-induced) conditions |
| GSM1428959 |
Hfq-bound RNA from -Vir (non-induced) conditions |
| GSM1428960 |
control from +Vir (virulence-induced) conditions |
| GSM1428961 |
Hfq-bound RNA from +Vir (virulence-induced) conditions |
|
| Relations |
| BioProject |
PRJNA254473 |
| SRA |
SRP044102 |
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