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Sample GSM197867 Query DataSets for GSM197867
Status Public on Apr 05, 2008
Title Pyr-LS Slide S3
Sample type RNA
 
Channel 1
Source name Cells grown with pyruvate fermentation
Organism Nitratidesulfovibrio vulgaris str. Hildenborough
Characteristics Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase with pyruvate as the only substrate; no sulfate was added.
Biomaterial provider Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Portugal
Treatment protocol Growth with pyruvate fermentation
Growth protocol He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
Extracted molecule total RNA
Extraction protocol He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
Label Cy5
Label protocol He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
 
Channel 2
Source name Cells grown with sulfate reduction
Organism Nitratidesulfovibrio vulgaris str. Hildenborough
Characteristics Desulfovibrio vulgaris batch culture was grown at 37 degree C to mid-log phase with sulfate as the only electron acceptor and lactate as the only electron donor
Biomaterial provider Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Portugal
Treatment protocol Growth with sulfate reduction
Growth protocol He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
Extracted molecule total RNA
Extraction protocol He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
Label Cy3
Label protocol He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
 
 
Hybridization protocol He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
Scan protocol He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
Description The objective of this study is to identify the genes differentially expressed in D. vulgaris under fermentative growth as compared to growth via dissimilatory sulfate reduction.
Data processing Lowess intensity-based normalization. He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P., Wall, J. D., Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72(6):4370-4381. PMID: 16751553, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed&term=16751553
 
Submission date Jun 04, 2007
Last update date Apr 04, 2008
Contact name Qiang He
E-mail(s) [email protected]
Phone 865-974-6067
Fax 865-974-2669
Organization name The University of Tennessee
Department Civil and Environmental Engineering
Lab Environmental Biotechnology
Street address 57A Perkins Hall
City Knoxville
State/province TN
ZIP/Postal code 37996-2010
Country USA
 
Platform ID GPL4071
Series (2)
GSE8015 Pyruvate fermentation vs Lactate-Sulfate
GSE8069 Energy metabolism pathways of the sulfate-reducer Desulfovibrio vulgaris Hildenborough

Data table header descriptions
ID_REF
VALUE normalized log2 ratios of CH1/CH2
CH1/CH2 Numerical ratios of CH1/CH2
Flags P-a good spot; A-a poor spot; M-a marginal spot; values are calculated only for good spots
CH1 Normalized signal intensity for channel 1
CH2 Normalized signal intensity for channel 2

Data table
ID_REF VALUE CH1/CH2 Flags CH1 CH2
1 -0.546725612 0.684572094 P 1651.3654 2412.2593
2 -0.054900034 0.962661144 P 1495.798 1553.8157
3 0.331747515 1.258536898 P 2165.094 1720.3262
4 1.09087386 2.130030163 P 14089.122 6614.5176
5 0.528050001 1.441978847 P 1032.4172 715.9725
6 0.287526843 1.220546147 P 6329.662 5185.926
7 0.98284073 1.976353107 P 1165.6165 589.7815
8 null
9 0.370417433 1.292726817 P 3934.7622 3043.7693
10 -0.056657871 0.961488914 P 17190.318 17878.852
11 1.092856446 2.132959313 P 1681.6023 788.3893
12 1.631558276 3.098474887 P 1184.9988 382.44583
13 0.48637892 1.400924222 P 1620.0743 1156.4325
14 -0.383721265 0.766458049 P 11127.149 14517.623
15 1.175429937 2.258601795 P 1076.29 476.52933
16 0.657053568 1.576858897 P 1317.1301 835.28723
17 0.010906749 1.007588631 P 1305.7996 1295.965
18 -0.070860517 0.952069952 P 1547.9474 1625.8757
19 0.498933386 1.413168392 P 1900.3695 1344.758
20 0.430540924 1.347738804 P 1957.3088 1452.2909

Total number of rows: 9216

Table truncated, full table size 288 Kbytes.




Supplementary file Size Download File type/resource
GSM197867_Cy3.txt.gz 907.7 Kb (ftp)(http) TXT
GSM197867_Cy5.txt.gz 902.5 Kb (ftp)(http) TXT
Processed data included within Sample table
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