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Sample GSM325928 Query DataSets for GSM325928
Status Public on Jan 06, 2009
Title wtBHI vs mutBALF 13626792
Sample type RNA
 
Channel 1
Source name wt BHI J4
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 mut BALF J7
Organism Actinobacillus pleuropneumoniae
Characteristics serotype 1 strain CM5 malT mutant
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 cDNA generated from the same condition but with a A. pleuropneumoniae serotype 1 strain CM5 mutant in gene malT
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) vincent.deslandes@umontreal.ca
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

Data table header descriptions
ID_REF
IA Net Intensity Value in Channel A (Cy3)
IB Net Intensity Value in Channel B (Cy5)
BkgA Background Channel A
BkgB Background Channel B
SDA Standard deviation for spot pixels in channel A
SDB Standard deviation for spot pixels in channel B
MedA Median Intensity Value in channel A
MedB Median Intensity Value in channel B
VALUE Log2 ratio (IB/IA)

Data table
ID_REF IA IB BkgA BkgB SDA SDB MedA MedB VALUE
1 497206 425213 165856 125414 2510.4 1682.1 2751 2005 -0.225658001
2 0 0 136122 109221 2610.6 1872.4 3299 2215 null
3 0 0 125097 108927 1748 1135.5 0 0 null
4 0 0 147186 108324 1925.4 1045.1 0 0 null
5 0 0 92064 81120 1736.8 918.4 1818 0 null
6 0 0 115676 86636 1814.6 1037.4 0 0 null
7 0 0 97857 99298 1490.1 1045.8 0 0 null
8 0 0 105840 95634 1598.5 1152.9 0 0 null
9 0 0 79255 93534 1537.6 1031.6 0 0 null
10 0 0 64782 93692 2047 1152.1 0 0 null
11 489363 513702 127946 122759 3033.3 3467.9 3088 3346 0.070026665
12 0 0 132756 151848 2381.6 2023.7 3040 1634 null
13 2546024 1042596 214630 116967 15660.8 6241 14466 6949 -1.288065789
14 0 0 218361 146861 15550.8 6715.2 12874 6355 null
15 0 0 134862 94164 1657 994.1 0 0 null
16 0 0 150750 100200 1757.7 1102.9 0 0 null
17 0 0 137004 89670 1584.7 949.6 0 0 null
18 0 0 98000 100125 1806.3 1084.9 1684 0 null
19 605642 468188 177906 115624 2956.2 2687.3 3583 2315 -0.371377299
20 0 0 162288 133329 3384.4 2850.6 3104 1983 null

Total number of rows: 5376

Table truncated, full table size 296 Kbytes.




Supplementary file Size Download File type/resource
GSM325928.mev.gz 310.4 Kb (ftp)(http) MEV
Processed data included within Sample table

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