|
Status |
Public on Dec 01, 2010 |
Title |
LitRvsControl_High_repl1 |
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 0.8
|
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 0.8
|
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 1 of 3 at OD600nm 0.8
|
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 |
|