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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 |
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Submission date |
Jun 06, 2012 |
Last update date |
Mar 02, 2016 |
Contact name |
Hans-Joachim Mollenkopf |
E-mail(s) |
mollenkopf@mpiib-berlin.mpg.de
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Phone |
+49 30 28460 482
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Organization name |
Max-Planck-Institute for Infection Biology
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Lab |
Microarray/Genomics Core Facility
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Street address |
Charitéplatz 1
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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 |