|
| Status |
Public on Dec 01, 2010 |
| Title |
LitRvsControl_Low_repl2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Aliivibrio salmonicida LFI1238 LitR mutant
|
| Organism |
Aliivibrio salmonicida LFI1238 |
| Characteristics |
genotype/variation: LitR mutant
strain: LFI1238
od: 600nm 0.15
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RNA-isol reagent (Fischer scientific). DNA was removed using the DNA-free kit (Ambion). Any traces of DNase were removed with the RNeasy Minelute Cleanup kit (Qiagen)
|
| Label |
Cy5
|
| Label protocol |
cDNA was generated and labelled with Cy3 and Cy5 by using 15 µg RNA, the Aminoallyl cDNA labeling kit (Ambion), and the CyDye™ Post-Labeling Reactive Dye Pack (GE Healthcare).
|
| |
|
| Channel 2 |
| Source name |
Aliivibrio salmonicida LFI1238 stimulated wild type control
|
| Organism |
Aliivibrio salmonicida LFI1238 |
| Characteristics |
genotype/variation: wild type
strain: LFI1238
od: 600nm 0.15
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RNA-isol reagent (Fischer scientific). DNA was removed using the DNA-free kit (Ambion). Any traces of DNase were removed with the RNeasy Minelute Cleanup kit (Qiagen)
|
| Label |
Cy3
|
| Label protocol |
cDNA was generated and labelled with Cy3 and Cy5 by using 15 µg RNA, the Aminoallyl cDNA labeling kit (Ambion), and the CyDye™ Post-Labeling Reactive Dye Pack (GE Healthcare).
|
| |
|
| |
| Hybridization protocol |
Samples were hybridised to the microarrays at 42 ºC on a TECAN HS4800 hybridisation station, and microarray slides were subsequently washed, once in 0.1×SSC/0.1% SDS for 5 min at 42 ºC, then once in 0.1×SSC/0.1% SDS for 11 min at room temperature, and finally four times in 0.1×SSC for 1 min at room temperature.
|
| Scan protocol |
Slides were scanned using a GenePix 4000B scanner (Axon Instruments Inc.)
Images were quantified using the GenePix v6.1 software
|
| Description |
Technical replicate 2 of 3 at OD600nm 0.15
|
| Data processing |
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. J-Express Pro v2.7 (Dysvik and Jonassen 2001) software was used.
|
| |
|
| Submission date |
Nov 22, 2010 |
| Last update date |
Nov 23, 2010 |
| Contact name |
Erik Hjerde |
| E-mail(s) |
erik.hjerde@uit.no
|
| Phone |
+47 77646263
|
| Organization name |
University of Tromsø
|
| Department |
Department of chemistry
|
| Street address |
Breivika
|
| City |
Tromsø |
| ZIP/Postal code |
9037 |
| Country |
Norway |
| |
|
| Platform ID |
GPL9985 |
| Series (2) |
| GSE25546 |
Prediction, microarray and Northern blot analyses identify new intergenic small RNAs in Aliivibrio salmonicida (wild type vs. LitR mutant) |
| GSE25558 |
Prediction, microarray and Northern blot analyses identify new intergenic small RNAs in Aliivibrio salmonicida |
|
