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| Status |
Public on Aug 16, 2007 |
| Title |
Heme_k2_Filtered bckg correct trans-norm |
| Platform organism |
Lactiplantibacillus plantarum WCFS1 |
| Sample organism |
Lactiplantibacillus plantarum |
| Experiment type |
Expression profiling by array
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| Summary |
We ran for each studied culture (WCFS1 NZ7608 NZ7602 and NZ7603) an independent shake flask cultivation and designed one experiment. The hybridization scheme (4 arrays) of the experiment was as follows: WCFS1_respiratory NZ7608_respiratory NZ7602_respiratory NZ7603_respiratory WCFS1_respiratory. In the experiment we studied the difference in response towards respiratory cultivation (OXYGEN HEME and VITAMIN K2) of each strain compared to wild type
Keywords: comparative genomic hybridization
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| Overall design |
Per array two cDNA labeled targets were hybridized on custom designed L. plantarum WCFS1 11K Agilent oligo microarrays (GEO Acc. Nr. GPL4318) using the Agilent 60-mer oligo microarray processing protocol version 4.1. An oligo-microarray contained an average of 3 probes per transcript. Dried slides were scanned in the Scan Array Express (PerkinElmer Life Sciences; Packard Bioscience) for both Cy3 and Cy5 at 10 microns and a PMT Gain between 40-50%. Spot intensity data was normalized and quantified (average intensity) using a customized grid in ImaGene (BioDiscovery, Inc.). Signal intensities of all probes were corrected against background in BioArray Software Environment (BASE). The ratio of each probe (M) was defined as log [cy5 intensity/cy3 intensity] where cy3 is the wild type. Fold change (FC) is defined as 2M. For the statistical analysis we used Linear Models for Microarray Analysis (Limma) (R/limma). Significant transcripts were defined as transcripts with a False Discovery Rate (FDR) adjusted for the pvalues of less than 1% and FC = 1.5
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| Contributor(s) |
Serrano LM, Molenaar D, Teusink B, de Vos WM, Smid EJ |
| Citation missing |
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| Submission date |
Aug 10, 2007 |
| Last update date |
Mar 17, 2012 |
| Contact name |
L. Mariela Serrano |
| Organization name |
TI Food and Nutrition
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| Street address |
Nieuwe Kanaal 9A
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| City |
Wageningen |
| ZIP/Postal code |
6709 PA |
| Country |
Netherlands |
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| Platforms (1) |
| GPL4318 |
WCFS Lactobacillus plantarum 11K 60-mer array, Version 1, our ID LPAG1 |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA102011 |
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