|
| Status |
Public on Dec 01, 2012 |
| Title |
Wild type in LB, replicate 3 |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
Wild type in LB
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
genotype: wild type
|
| Treatment protocol |
The cells were treated with cold ethanol 20%, phenol 1% and left 30min on ice prior to centrifugation.
|
| Growth protocol |
The media was inoculated with 1/1000 of an overnight culture and grown to OD600=0.3 at 37 C upon 200rpm agitation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Promega SV total RNA extraction kit following the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
Total RNA (10 μg) was converted to cDNA and fluorescently labelled by random priming to incorporate Cy5-dCTP (Amersham) using reverse transcriptase (StrataScript, Stratagene).
|
| |
|
| Channel 2 |
| Source name |
Wild type in LB
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
genotype: wild type
|
| Treatment protocol |
The cells were treated with cold ethanol 20%, phenol 1% and left 30min on ice prior to centrifugation.
|
| Growth protocol |
The media was inoculated with 1/1000 of an overnight culture and grown to OD600=0.3 at 37 C upon 200rpm agitation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted.
|
| Label |
Cy3
|
| Label protocol |
Genomic DNA was labeled with Cy3.
|
| |
|
| |
| Hybridization protocol |
Slides were blocked with DCE according to the protocol in PMID 11266573. For hybridisation and washing protocols, see www.ifr.ac.uk/safety/Microarrays/default.html#protocols.
|
| Scan protocol |
Scanned on a GenePix 4000A scanner (Axon Instruments, Inc.). Images were quantified using Axon GenePix Pro7.
|
| Description |
WT_3
|
| Data processing |
Spots showing a reference signal lower than background plus two standard deviations or obvious blemishes were excluded from subsequent analyses. Local background was subtracted from spot signals, and fluorescence ratios were calculated. To compensate for unequal dye incorporation or any effect of the amount of template, data centering was performed by bringing the median natural logarithm of the ratios for each group of spots printed by the same pin to zero.
|
| |
|
| Submission date |
Feb 20, 2012 |
| Last update date |
Dec 01, 2012 |
| Contact name |
Gary Rowley |
| E-mail(s) |
g.rowley@uea.ac.uk
|
| Organization name |
University of East Anglia
|
| Department |
School of Biological Sciences
|
| Street address |
Norwich Research Park
|
| City |
norwich |
| ZIP/Postal code |
NR4 7TJ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL5780 |
| Series (1) |
| GSE35938 |
Transcriptome analysis of the Salmonella enterica OmpR regulon |
|
