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Sample GSM678559 Query DataSets for GSM678559
Status Public on Jul 01, 2011
Title B. breve UCC2003 grown in MRS vs B. breve UCC2003 grown in vivo experiment 1
Sample type mixed
 
Channel 1
Source name Bifidobacterium breve UCC2003 grown in MRS
Organism Bifidobacterium breve UCC2003
Characteristics strain: UCC2003
growth stage: exponential
od600: 0.5
carbon source: glucose
Biomaterial provider Douwe van Sinderen, Department of Microbiology, University College Cork, Ireland
Treatment protocol Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).
Growth protocol Bifidobacterium breve UCC200 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of glucose solution as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5 .
Extracted molecule total RNA
Extraction protocol RNA isolation, RNA quality control was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).
Label Cy3
Label protocol cDNA from total RNA was synthesized using the cDNA synthesis and labelling kit DSK-001 (Kreatech) according to the manufacturer’s instructions
1 μl of each cDNA solution was labelled with Cy3 using Cy3-ULS from the cDNA synthesis and labelling kit DSK-001 (Kreatech, Amsterdam, The Netherlands) according to the manufacterers instructions.
 
Channel 2
Source name ceaca of Balb/C mice colonized with B. breve UCC2003
Organism Mus musculus
Characteristics strain: UCC2003
source tissue: Mus musculus balb/c ceacum
age: 25 days
Biomaterial provider Douwe van Sinderen, Department of Microbiology, University College Cork, Ireland
Treatment protocol Caeca, isolated from mice, were placed in RNAlater (Ambion) and immediately processed. Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77)
Growth protocol Seven-week-old male, BalbC mice were housed in individually vented cages (Animal care systems, Colorado) under a strict 12 h light cycle. Mice (n = 5 per group) were fed a standard polysaccharide-rich mouse chow diet and water ad libidum. Mice were inoculated by oral gavage (109 cfu of B. breve UCC2003 pPKCM7 in 100 ul of PBS ). Fecal pellets were collected at intervals over 25 days to enumerate bacteria. Twenty five days after inoculation, mice were sacrificed and their intestinal tracts quickly dissected. Aliquots of small intestine, caecum and large intestine were harvested for determination of colony forming units (cfu) (serial dilution plating on RCA agar plates with appropriate antibiotics). Caeca were placed in RNAlater for immediate RNA isolation.
Extracted molecule total RNA
Extraction protocol Bacterial mRNA was extracted from caecal RNA preparations using the MicrobEnrich and MicrobExpress kits (Ambion) according to the manufacturer’s instructions. cDNA from bacterial mRNA was synthesized using the cDNA synthesis and labelling kit DSK-001 (Kreatech) according to the manufacturer’s instructions.
Label Cy5
Label protocol 1 μl of each cDNA solution (10 ng) was amplified in triplicate using the GenomiPhi™ V2 DNA Amplification Kit (Amersham Biosciences) according to the manufacturer's protocol and labelled with Cy5 using Cy5-ULS from the cDNA synthesis and labelling kit DSK-001 (Kreatech).
 
 
Hybridization protocol Labelled and amplified cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis (v4.0) manual (publication number G4140-90050).
Scan protocol Following hybridization, microarrays were washed as described in the manuals and scanned using Agilent's DNA microarray scanner G2565A.
Data processing The scanning results were converted to data files with Agilent's Feature Extraction software (version 9.5) using standard settings as described in the Agilent's Feature Extraction manual.
 
Submission date Feb 23, 2011
Last update date Jul 01, 2011
Contact name Aldert Zomer
E-mail(s) A.L.Zomer@uu.nl
Organization name Utrecht University
Department Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine
Street address Yalelaan 1
City Utrecht
ZIP/Postal code 3584 cl
Country Netherlands
 
Platform ID GPL13210
Series (1)
GSE27491 Functional genome analysis of Bifidobacterium breve UCC2003 reveals a major conserved host-colonization factor

Data table header descriptions
ID_REF
VALUE Agilent default normalized log 10 ratio of Cy5/Cy3 signals

Data table
ID_REF VALUE
1 3.408573311
2 1.245404695
3 0.987758069
4 1.148673983
5 0.836790553
6 0.945395125
7 1.06981014
8 1.004921498
9 1.057196359
10 0.848663083
11 0.93012075
12 0.305985701
13 0.198708883
14 -0.367926963
15 -0.43573521
16 0.111850741
17 -1.601369949
18 0.023994988
19 0.051627876
20 -0.161597747

Total number of rows: 45220

Table truncated, full table size 794 Kbytes.




Supplementary file Size Download File type/resource
GSM678559_3_Microarray_252057310019_S02_CGH_v4_95_Feb07_3_1_2.txt.gz 13.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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