|
Status |
Public on Mar 24, 2015 |
Title |
pBAD-RprA 2 |
Sample type |
mixed |
|
|
Channel 1 |
Source name |
Salmonella enterica SL1344
|
Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
Characteristics |
vector: pBAD-RprA
|
Treatment protocol |
At OD=1.5, 0.2% (final conc.) L-arabinose was added. Total RNA was isolated 10 min post treatment.
|
Growth protocol |
Salmonella carrying pBAD-ctr, pBAD-RprA or pBAD-RprA-proc. were grown in LB-media to OD=1.5.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
SV40 RNA isolation Kit (promega). GenomicDNA was extracted using the Qiagen 'Genomic DNA' Kit
|
Label |
Cy5
|
Label protocol |
total RNA was labelled with Cy3 using random hexamers and reverse transcriptase (Stratagene AffinityScript) while genomicDNA was labelled with Cy5 using the Invitrogen BioPrime DNA Labeling System
|
|
|
Channel 2 |
Source name |
Salmonella enterica SL1344
|
Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
Characteristics |
vector: pBAD-RprA
|
Treatment protocol |
At OD=1.5, 0.2% (final conc.) L-arabinose was added. Total RNA was isolated 10 min post treatment.
|
Growth protocol |
Salmonella carrying pBAD-ctr, pBAD-RprA or pBAD-RprA-proc. were grown in LB-media to OD=1.5.
|
Extracted molecule |
total RNA |
Extraction protocol |
SV40 RNA isolation Kit (promega). GenomicDNA was extracted using the Qiagen 'Genomic DNA' Kit
|
Label |
Cy3
|
Label protocol |
total RNA was labelled with Cy3 using random hexamers and reverse transcriptase (Stratagene AffinityScript) while genomicDNA was labelled with Cy5 using the Invitrogen BioPrime DNA Labeling System
|
|
|
|
Hybridization protocol |
Microarray slide were hybridized in a water bath over night at 63C. For detailed protocol see: http://www.ifr.ac.uk/safety/Microarrays/default.html#protocols
|
Scan protocol |
Axon GenePix4000A, 10nm resolution scan
|
Data processing |
Data centring was performed by bringing the median ratio (Cy5/Cy3) for each of the 16 blocks to one using the following equation: (Ti) = (Cy5i/Cy3i) - c, where T is the centred ratio, i is the gene index, Cy5 and Cy3 are the red and green intensities and c is the 50th percentile of all Cy5/Cy3 ratios. pBAD-ctrA serves as control for pBAD-RprA, pBAD-ctrB is control for pBAD-RprA-proc.
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|
|
Submission date |
Mar 23, 2015 |
Last update date |
Mar 24, 2015 |
Contact name |
Kai Papenfort |
Organization name |
IMIB Würzburg
|
Department |
RNA Biology
|
Street address |
Josef-Schneider Str.2/BAU D15
|
City |
Würzburg |
State/province |
Würzburg |
ZIP/Postal code |
97080 |
Country |
Germany |
|
|
Platform ID |
GPL5780 |
Series (1) |
GSE67187 |
A small RNA controlled AND-gate regulates extrachromosomal DNA transfer in Salmonella |
|