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Sample GSM251042 Query DataSets for GSM251042
Status Public on Apr 21, 2008
Title F-M_C089 Replicate 1
Sample type genomic
 
Channel 1
Source name F-M_C089 genomic DNA
Organism Campylobacter jejuni
Characteristics Strain F-M_C089
Growth protocol Cells from each strain were grown as a confluent lawn on Mueller-Hinton agar plates at 42ºC for 36 Hrs. under microaerophilic conditions prior to genomic DNA isolation
Extracted molecule genomic DNA
Extraction protocol Approximately 1X10^10 cells were harvested and genomic DNA extracted by modified lysis/phenol extraction protocol as described in Taboada et al (2004) J Clin Micro 42:4566-4576.
Label Cy3
Label protocol Approximately 2 µg of genomic DNA was labeled by chemical coupling to Label IT Cy dye as described in Taboada et al (2004) J Clin Micro 42:4566-4576.
 
Channel 2
Source name NCTC_11168 genomic DNA
Organism Campylobacter jejuni
Characteristics Strain NCTC_11168
Growth protocol Cells from each strain were grown as a confluent lawn on Mueller-Hinton agar plates at 42ºC for 36 Hrs. under microaerophilic conditions prior to genomic DNA isolation
Extracted molecule genomic DNA
Extraction protocol Approximately 1X10^10 cells were harvested and genomic DNA extracted by modified lysis/phenol extraction protocol as described in Taboada et al (2004) J Clin Micro 42:4566-4576.
Label Cy5
Label protocol Approximately 2 µg of genomic DNA was labeled by chemical coupling to Label IT Cy dye as described in Taboada et al (2004) J Clin Micro 42:4566-4576.
 
 
Hybridization protocol Equivalent amounts of Cy-3 labelled experimental and Cy-5 labelled control genomic DNAs with similar dye incorporation efficiencies were pooled and co-hybridized overnight to the microarray at 37ºC in DIG-easy hyb solution (Roche). Washes performed as described in Taboada et al (2004) J Clin Micro 42:4566-4576.
Scan protocol Microarrays were scanned using a Chipreader laser scanner (BioRad, Mississauga, ON) according to the manufacturer’s recommendations. Laser power and gain were adjusted to obtain balanced scans on control spots.
Description CGH analysis of Strain F-M_C089 vs. Strain NCTC_11168
Data processing Features were extracted using ArrayPro Analyzer version 4.5 and imported into the BioArray Software Environment (BASE version 1.2). Spots flagged due to poor spot morphology or low signal intensity (less than 3 X local background) were filtered out. After print-tip Loess normalization, data was used to calculate the average log ratio [log2(Signal Experimental / Signal Control)] of replicate spots
 
Submission date Dec 17, 2007
Last update date Dec 17, 2007
Contact name Eduardo N Taboada
E-mail(s) eduardo_taboada@phac-aspc.gc.ca
Phone +1 (403)-382-5550
Fax +1 (403)-381-1202
Organization name Public Health Agency of Canada
Lab Laboratory for Foodborne Zoonoses
Street address PO Box 640, TWP Rd. 9-1
City Lethbridge
State/province Alberta
ZIP/Postal code T1J 3Z4
Country Canada
 
Platform ID GPL2681
Series (1)
GSE9919 CGH analysis of Campylobacter jejuni isolates previously analyzed by Multi-Locus Sequence Typing

Data table header descriptions
ID_REF
VALUE Loess normalized log2 ratio (experimental/control)

Data table
ID_REF VALUE
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20

Total number of rows: 4608

Table truncated, full table size 68 Kbytes.




Supplementary file Size Download File type/resource
GSM251042.txt.gz 124.5 Kb (ftp)(http) TXT
Processed data included within Sample table

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