|
| Status |
Public on Jan 06, 2009 |
| Title |
wtBHi vs wt BALF, 13623129 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
wt BHI B2.1
|
| Organism |
Actinobacillus pleuropneumoniae |
| Characteristics |
serotype 1 strain CM5
bacteria grown in BHI broth to OD600 of 0.7 followed by subsequent incubation in fresh BHI broth for 30 min.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol reagent as prescribed.
|
| Label |
Cy3
|
| Label protocol |
RNA was reverse-transcribed to cDNA, using Invitrogen's SuperScript II and amino-allyl dUTP. Samples were then indirectly labelled with Cy3 or Cy5 esters. Complete protocol is described in :
Carrillo CD, Taboada E, Nash JH, Lanthier P, Kelly J, Lau PC, Verhulp R, Mykytczuk O, Sy J, Findlay WA et al: Genome-wide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. J Biol Chem 2004, 279(19):20327-20338.
|
| |
|
| Channel 2 |
| Source name |
wt BALF B5.1
|
| Organism |
Actinobacillus pleuropneumoniae |
| Characteristics |
serotype 1 strain CM5
bacteria grown in BHI broth to OD600 of 0.7 followed by 30 min. incubation in warmed BALF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol reagent as prescribed.
|
| Label |
Cy5
|
| Label protocol |
RNA was reverse-transcribed to cDNA, using Invitrogen's SuperScript II and amino-allyl dUTP. Samples were then indirectly labelled with Cy3 or Cy5 esters. Complete protocol is described in :
Carrillo CD, Taboada E, Nash JH, Lanthier P, Kelly J, Lau PC, Verhulp R, Mykytczuk O, Sy J, Findlay WA et al: Genome-wide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. J Biol Chem 2004, 279(19):20327-20338.
|
| |
|
| |
| Hybridization protocol |
Complete protocol is described in :
Carrillo CD, Taboada E, Nash JH, Lanthier P, Kelly J, Lau PC, Verhulp R, Mykytczuk O, Sy J, Findlay WA et al: Genome-wide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. J Biol Chem 2004, 279(19):20327-20338.
|
| Scan protocol |
Arrays were scanned with a Perkins Elmer ScanArray, and data was acquired using SpotFinder v3.1.1.
|
| Description |
Competitive hybridization of cDNA generated from A. pleuropneumoniae serotype 1 strain CM5 RNA extracted after growth in BHI broth and subsequent incubation in either fresh BHi broth or BALF.
|
| Data processing |
NORMALIZATION WITH MIDAS :
- One Bad Channel Tolerance Policy parameter on how to deal with one-bad-channel spots = Generous
- Net intensities were normalized using Lowess algorithm (MIDAS). Mode = block, smoothing parameter = 0.33, reference = Cy3
- In slide replicate analysis to merge data with same unique identifier
|
| |
|
| Submission date |
Oct 01, 2008 |
| Last update date |
Oct 08, 2008 |
| Contact name |
Vincent Deslandes |
| E-mail(s) |
[email protected]
|
| Organization name |
Université de Montréal - Faculté de Médecine Vétérinaire
|
| Department |
Groupe de Recherche sur les Maladies Infectieuses du Porc
|
| Street address |
3200 rue Sicotte
|
| City |
St-Hyacinthe |
| State/province |
Quebec |
| ZIP/Postal code |
J2S7C6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6658 |
| Series (1) |
| GSE13006 |
Transcript profiling of Actinobacillus pleuropneumoniae in BALF |
|
