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Sample GSM3074526 Query DataSets for GSM3074526
Status Public on Mar 03, 2021
Title B. animalis subsp. animalis CNCM I-4602 grown in RSM with cysteine vs. grown in modified MRS with glucose
Sample type RNA
 
Channel 1
Source name B. animalis subsp. animalis CNCM I-4602 grown in RSM with cysteine
Organism Bifidobacterium animalis subsp. animalis
Characteristics genotype: wild type
Growth protocol Bifidobacterium animalis subsp. animalis CNCM I-4602 was grown in modified de Man, Rogosa and Sharpe (MRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and containing 0.5% to an OD of 0.5 glucose or in reconsituted skimmed milk containing 0.5 % glucose to a pH of 5.3.
Extracted molecule total RNA
Extraction protocol Bifidobacterial cells were isolated from milk-based medium (RSM) according to a previously described method (de Jong et al., 2013). 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). RNA isolation, RNA quality control and complementary DNA synthesis 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 Labelling 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).
 
Channel 2
Source name B. animalis subsp. animalis CNCM I-4602 grown in modified MRS with glucose
Organism Bifidobacterium animalis subsp. animalis
Characteristics genotype: wild type
Growth protocol Bifidobacterium animalis subsp. animalis CNCM I-4602 was grown in modified de Man, Rogosa and Sharpe (MRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and containing 0.5% to an OD of 0.5 glucose or in reconsituted skimmed milk containing 0.5 % glucose to a pH of 5.3.
Extracted molecule total RNA
Extraction protocol Bifidobacterial cells were isolated from milk-based medium (RSM) according to a previously described method (de Jong et al., 2013). 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). RNA isolation, RNA quality control and complementary DNA synthesis 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 Cy5
Label protocol Labelling 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).
 
 
Hybridization protocol Labelled 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 (G4140-90050).
Scan protocol Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).
Description Gene expression array
Data processing Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).
 
Submission date Apr 03, 2018
Last update date Mar 04, 2021
Contact name Francesca Bottacini
Organization name University College Cork
Department APC Microbiome Institute & School of Microbiology
Street address Western Road
City Cork
ZIP/Postal code ND
Country Ireland
 
Platform ID GPL24807
Series (1)
GSE112626 Comprehensive genomic, phenotypic and transcriptomic approaches to enhance Bifidobacterium animalis subsp. animalis growth and survival in milk

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 2.694096565e-001
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 5.189546224e-002
13 1.016340866e-001
14 -6.501589430e-002
15 4.478932253e-001
16 7.068639163e-002
17 1.087944435e-001
18 -5.892407904e-002
19 4.077573345e-002
20 1.965920831e-001

Total number of rows: 45220

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM3074526_Sample4-raw-data.txt.gz 12.7 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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