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| Status |
Public on Dec 01, 2015 |
| Title |
Targets of the small regulatory RNA DapZ |
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Experiment type |
Expression profiling by array
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| Summary |
To determine the targets of the small regulatory RNA DapZ in S. Typhimurium, we looked at the effect of a short pulse of DapZ over-expression on the Salmonella transcriptome, as well as a DapZ variant that lacks the GcvB-like R1 region. To achieve over-expression, the wild-type DapZ and its variant were cloned in the pBAD plasmid and induced with 0.2% L-arabinose for 10 min. We then extracted the total RNA for transcriptional profiling. A strain carrying the pBAD plasmid w/o insert was used as negative control (also induced by L-arabinose). 2 biological replicates were performed. This sRNA target identification strategy has been described in Papenfort et al; Molecular Microbiology (2006) 62(6), 1674-1688.
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| Overall design |
We used whole-genome S. typhimurium microarrays to determine relative mRNA expression changes, comparing the mRNA profiles. Microarrays used in this study were produced by in-situ synthesis as 8x15k multipack format from Agilent Technologies. Each microarray comprises 13268 60-mer S. typhimurium strain SL1344 specific oligonucleotides supplemented with 319 60-mer S. enterica subsp. serovar Typhimurium 14028S specific oligonucleotides, 360 60-mer S. typhimurium LT2 specific oligonucleotides and 360 60-mer oligonucleotides specific for 149 Salmonella sRNAs. The experimental design involves the use of Salmonella enterica serovar Typhimurium genomic DNA as the co-hybridized control for one channel on all microarrays. Two independent biological eperiments were analyzed.
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| Contributor(s) |
Chao Y, Mollenkopf H, Pappenfort K, Vogel J |
| Citation(s) |
22922465 |
| |
| Submission date |
Jun 06, 2012 |
| Last update date |
Mar 02, 2016 |
| Contact name |
Hans-Joachim Mollenkopf |
| E-mail(s) |
mollenkopf@mpiib-berlin.mpg.de
|
| Phone |
+49 30 28460 482
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| Organization name |
Max-Planck-Institute for Infection Biology
|
| Lab |
Microarray/Genomics Core Facility
|
| Street address |
Charitéplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
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| Platforms (1) |
| GPL11416 |
SALSIFY, Agilent-026881 S. Typhimurim |
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| Samples (6)
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| GSM944527 |
delta dapZ with pBAD-ctr (sample 1) |
| GSM944531 |
delta dapZ with pBAD-ctr (sample 2) |
| GSM944532 |
delta dapZ with pBAD DapZ (sample 1) |
| GSM944533 |
delta dapZ with pBAD DapZ (sample 2) |
| GSM944534 |
delta dapZ with pBAD DapZ GU (sample 1) |
| GSM944559 |
delta dapZ with pBAD DapZ GU (sample 2) |
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| Relations |
| BioProject |
PRJNA168103 |
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